Chapter 5 Community composition
5.1 Taxonomy overview
Mean percentage of Bacteria and Archaea in the samples
domain_summary <- genome_counts_filt %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS normalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>%
left_join(sample_metadata, by = join_by(sample == sample)) %>%
left_join(genome_metadata, by = join_by(genome == genome)) %>%
group_by(sample,domain) %>%
summarise(relabun=sum(count))
domain_summary %>%
group_by(domain) %>%
summarise(mean=mean(relabun, na.rm=T)*100,sd=sd(relabun, na.rm=T)*100) %>%
arrange(-mean) %>%
tt()| domain | mean | sd |
|---|---|---|
| d__Bacteria | 99.5141306 | 1.71795 |
| d__Archaea | 0.4858694 | 1.71795 |
#ggsave("figures/mtcars.png", width = 10, height = 6)
genome_counts_filt %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS normalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(., genome_metadata, by = join_by(genome == genome)) %>% #append genome metadata
left_join(., sample_metadata, by = join_by(sample == sample)) %>% #append sample metadata
filter(count > 0) %>% #filter 0 counts
# filter(!region %in% c("Eskoriatza","Villabona")) %>%
mutate(season=factor(season,levels=c("spring","autumn"))) %>%
ggplot(., aes(x=sample,y=count, fill=phylum, group=phylum)) + #grouping enables keeping the same sorting of taxonomic units
geom_bar(stat="identity", colour="white", linewidth=0.1, show.legend = FALSE) + #plot stacked bars with white borders
scale_fill_manual(values=phylum_colors) +
facet_nested(. ~ type + region+season, scales="free") + #facet per day and treatment
guides(fill = guide_legend(ncol = 2)) +
theme(axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.x = element_blank(),
panel.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(linewidth = 0.5, linetype = "solid", colour = "black"),
panel.border = element_rect(colour = "black", fill = NA),
strip.background = element_rect(fill = "white", color = "black"),
strip.text = element_text(size = 8, lineheight = 0.6)) +
labs(fill="Phylum",y = "Relative abundance",x="Samples")
Number of bacteria phyla
[1] 27Bacteria phyla in natural ponds
phylum
EHA02325_bin.10 p__Bacillota_A
EHA02325_bin.13 p__Pseudomonadota
EHA02325_bin.39 p__Bacteroidota
EHA02329_bin.18 p__Verrucomicrobiota
EHA02330_bin.9 p__Cyanobacteriota
EHA02331_bin.2 p__Bacillota
EHA02336_bin.41 p__Bacillota_C
EHA02338_bin.7 p__Desulfobacterota
EHA02341_bin.14 p__Spirochaetota
EHA02343_bin.12 p__Acidobacteriota
EHA02355_bin.3 p__Bacillota_B
EHA02388_bin.85 p__Deferribacterota
EHA02392_bin.43 p__Chloroflexota
EHA02398_bin.48 p__Fusobacteriota
EHA02398_bin.53 p__Campylobacterota
EHA04294_bin.16 p__Desulfobacterota_F
EHA04302_bin.12 p__Patescibacteria
EHA04302_bin.18 p__J088
EHA04321_bin.47 p__Planctomycetota
EHA04321_bin.50 p__Omnitrophota
EHA04321_bin.55 p__Chlamydiota
EHA04321_bin.69 p__Actinomycetota
EHA04337_bin.58 p__Desulfobacterota_G
EHA04343_bin.186 p__Bacteria phyla in protected ponds
phylum
EHA02325_bin.10 p__Bacillota_A
EHA02325_bin.13 p__Pseudomonadota
EHA02325_bin.19 p__Bacteroidota
EHA02329_bin.18 p__Verrucomicrobiota
EHA02330_bin.9 p__Cyanobacteriota
EHA02331_bin.2 p__Bacillota
EHA02336_bin.41 p__Bacillota_C
EHA02338_bin.7 p__Desulfobacterota
EHA02355_bin.3 p__Bacillota_B
EHA02374_bin.97 p__Fusobacteriota
EHA02388_bin.64 p__Chloroflexota
EHA02388_bin.85 p__Deferribacterota
EHA04305_bin.59 p__Spirochaetota
EHA04352_bin.62 p__CampylobacterotaBacteria phyla in urban ponds
phylum
EHA02325_bin.10 p__Bacillota_A
EHA02325_bin.13 p__Pseudomonadota
EHA02325_bin.39 p__Bacteroidota
EHA02329_bin.18 p__Verrucomicrobiota
EHA02331_bin.2 p__Bacillota
EHA02336_bin.41 p__Bacillota_C
EHA02338_bin.7 p__Desulfobacterota
EHA02340_bin.1 p__Cyanobacteriota
EHA02341_bin.14 p__Spirochaetota
EHA02341_bin.28 p__Fusobacteriota
EHA02355_bin.3 p__Bacillota_B
EHA02378_bin.75 p__Deferribacterota
EHA02398_bin.53 p__Campylobacterota
EHA04304_bin.13 p__JAKLEM01
EHA04304_bin.1 p__Patescibacteria
EHA04304_bin.21 p__Chloroflexota
EHA04321_bin.69 p__Actinomycetota
EHA04337_bin.116 p__Acidobacteriota
EHA04337_bin.35 p__Fibrobacterota
EHA04337_bin.58 p__Desulfobacterota_G
EHA04337_bin.88 p__Myxococcota
EHA04343_bin.186 p__Number of Archaea phyla
[1] 5Archaea phyla in natural ponds
phylum
EHA02392_bin.10 p__Methanobacteriota
EHA04302_bin.11 p__Nanoarchaeota
EHA04304_bin.19 p__Halobacteriota
EHA04321_bin.111 p__Iainarchaeota
EHA04343_bin.4 p__ThermoproteotaArchaea phyla in protected ponds
phylum
EHA04312_bin.192 p__Halobacteriota
EHA04352_bin.100 p__ThermoproteotaArchaea phyla in urban ponds
phylum
EHA02392_bin.10 p__Methanobacteriota
EHA04304_bin.19 p__Halobacteriota5.2 Phylum relative abundances
phylum_summary <- genome_counts_filt %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>%
left_join(sample_metadata, by = join_by(sample == sample)) %>%
left_join(genome_metadata, by = join_by(genome == genome)) %>%
group_by(sample,phylum,type, season) %>%
summarise(relabun=sum(count))phylum_summary %>%
group_by(phylum) %>%
summarise(total_mean=mean(relabun*100, na.rm=T),
total_sd=sd(relabun*100, na.rm=T)) %>%
mutate(total=str_c(round(total_mean,2),"±",round(total_sd,2))) %>%
arrange(-total_mean) %>%
dplyr::select(phylum,total) %>%
tt()| phylum | total |
|---|---|
| p__Bacteroidota | 53.53±20.47 |
| p__Bacillota_A | 15.07±11.48 |
| p__Pseudomonadota | 13.1±18.44 |
| p__Bacillota | 5.62±7.54 |
| p__Verrucomicrobiota | 4.16±5.07 |
| p__Desulfobacterota | 2.11±2.92 |
| p__Cyanobacteriota | 1.4±6.77 |
| p__Chloroflexota | 1.04±3.88 |
| p__Fusobacteriota | 0.52±1.23 |
| p__Myxococcota | 0.5±4.84 |
| p__Bacillota_C | 0.47±0.77 |
| p__Patescibacteria | 0.37±1.58 |
| p__Acidobacteriota | 0.34±1.44 |
| p__Deferribacterota | 0.31±0.9 |
| p__Bacillota_B | 0.24±0.36 |
| p__Desulfobacterota_F | 0.23±1.04 |
| p__Halobacteriota | 0.21±1.41 |
| p__Planctomycetota | 0.17±1.16 |
| p__Thermoproteota | 0.15±0.55 |
| p__Nanoarchaeota | 0.07±0.65 |
| p__Spirochaetota | 0.07±0.31 |
| p__Campylobacterota | 0.06±0.3 |
| p__Methanobacteriota | 0.04±0.28 |
| p__Actinomycetota | 0.04±0.2 |
| p__Fibrobacterota | 0.04±0.35 |
| p__ | 0.04±0.29 |
| p__Chlamydiota | 0.03±0.14 |
| p__Desulfobacterota_G | 0.03±0.2 |
| p__J088 | 0.02±0.11 |
| p__Iainarchaeota | 0.01±0.1 |
| p__JAKLEM01 | 0.01±0.11 |
| p__Omnitrophota | 0.01±0.05 |
phylum_arrange <- phylum_summary %>%
group_by(phylum) %>%
summarise(mean=mean(relabun)) %>%
arrange(-mean) %>%
dplyr::select(phylum) %>%
pull()
phylum_summary %>%
filter(phylum %in% phylum_arrange) %>%
mutate(phylum=factor(phylum,levels=rev(phylum_arrange))) %>%
ggplot(aes(x=relabun, y=phylum, group=phylum, color=phylum)) +
scale_color_manual(values=phylum_colors[rev(phylum_arrange)]) +
geom_jitter(alpha=0.5, show.legend = FALSE) +
theme_minimal() +
theme(legend.position="none") +
labs(y="Phylum",x="Relative abundance")
5.2.1 Per pond
phylum_summary %>%
group_by(phylum) %>%
summarise(total_mean=mean(relabun*100, na.rm=T),
total_sd=sd(relabun*100, na.rm=T),
natural_mean=mean(relabun[type=="natural"]*100, na.rm=T),
natural_sd=sd(relabun[type=="natural"]*100, na.rm=T),
protected_mean=mean(relabun[type=="protected"]*100, na.rm=T),
protected_sd=sd(relabun[type=="protected"]*100, na.rm=T),
urban_mean=mean(relabun[type=="urban"]*100, na.rm=T),
urban_sd=sd(relabun[type=="urban"]*100, na.rm=T)) %>%
mutate(total=str_c(round(total_mean,2),"±",round(total_sd,2)),
natural=str_c(round(natural_mean,2),"±",round(natural_sd,2)),
protected=str_c(round(protected_mean,2),"±",round(protected_sd,2)),
urban=str_c(round(urban_mean,2),"±",round(urban_sd,2))) %>%
arrange(-total_mean) %>%
dplyr::select(phylum,total,natural,protected,urban) %>%
tt()| phylum | total | natural | protected | urban |
|---|---|---|---|---|
| p__Bacteroidota | 53.53±20.47 | 50.72±21.6 | 57.47±21.28 | 53.47±17.18 |
| p__Bacillota_A | 15.07±11.48 | 11.93±9.38 | 19.02±15.51 | 15.52±6.64 |
| p__Pseudomonadota | 13.1±18.44 | 15.4±21.12 | 11.62±18.14 | 10.95±13.43 |
| p__Bacillota | 5.62±7.54 | 7.41±9.62 | 3.76±4.74 | 4.85±5.6 |
| p__Verrucomicrobiota | 4.16±5.07 | 5.14±5.61 | 3.09±4.44 | 3.82±4.69 |
| p__Desulfobacterota | 2.11±2.92 | 1.51±1.68 | 1.51±1.92 | 3.91±4.59 |
| p__Cyanobacteriota | 1.4±6.77 | 2.03±9.69 | 1.08±4.04 | 0.69±0.83 |
| p__Chloroflexota | 1.04±3.88 | 1.23±2.97 | 0.69±3.69 | 1.13±5.38 |
| p__Fusobacteriota | 0.52±1.23 | 0.26±0.51 | 0.45±1.36 | 1.05±1.74 |
| p__Myxococcota | 0.5±4.84 | 0±0 | 0±0 | 2.02±9.68 |
| p__Bacillota_C | 0.47±0.77 | 0.39±0.72 | 0.71±1.04 | 0.31±0.27 |
| p__Patescibacteria | 0.37±1.58 | 0.81±2.31 | 0±0 | 0.1±0.46 |
| p__Acidobacteriota | 0.34±1.44 | 0.58±2 | 0±0 | 0.33±1.11 |
| p__Deferribacterota | 0.31±0.9 | 0.52±1.33 | 0.12±0.21 | 0.17±0.24 |
| p__Bacillota_B | 0.24±0.36 | 0.08±0.22 | 0.32±0.31 | 0.43±0.48 |
| p__Desulfobacterota_F | 0.23±1.04 | 0.53±1.54 | 0±0 | 0±0 |
| p__Halobacteriota | 0.21±1.41 | 0.09±0.27 | 0.04±0.18 | 0.62±2.8 |
| p__Planctomycetota | 0.17±1.16 | 0.39±1.75 | 0±0 | 0±0 |
| p__Thermoproteota | 0.15±0.55 | 0.28±0.78 | 0.1±0.29 | 0±0 |
| p__Nanoarchaeota | 0.07±0.65 | 0.17±0.99 | 0±0 | 0±0 |
| p__Spirochaetota | 0.07±0.31 | 0.02±0.07 | 0.02±0.09 | 0.24±0.59 |
| p__Campylobacterota | 0.06±0.3 | 0.1±0.43 | 0.01±0.03 | 0.07±0.22 |
| p__Methanobacteriota | 0.04±0.28 | 0.09±0.42 | 0±0 | 0.01±0.05 |
| p__Actinomycetota | 0.04±0.2 | 0.08±0.3 | 0±0 | 0.01±0.02 |
| p__Fibrobacterota | 0.04±0.35 | 0±0 | 0±0 | 0.14±0.69 |
| p__ | 0.04±0.29 | 0.07±0.44 | 0±0 | 0.02±0.09 |
| p__Chlamydiota | 0.03±0.14 | 0.06±0.21 | 0±0 | 0±0 |
| p__Desulfobacterota_G | 0.03±0.2 | 0.01±0.08 | 0±0 | 0.08±0.39 |
| p__J088 | 0.02±0.11 | 0.05±0.17 | 0±0 | 0±0 |
| p__Iainarchaeota | 0.01±0.1 | 0.03±0.15 | 0±0 | 0±0 |
| p__JAKLEM01 | 0.01±0.11 | 0±0 | 0±0 | 0.05±0.22 |
| p__Omnitrophota | 0.01±0.05 | 0.02±0.07 | 0±0 | 0±0 |
phylum_summary %>%
filter(phylum %in% phylum_arrange) %>%
mutate(phylum=factor(phylum,levels=rev(phylum_arrange))) %>%
filter(relabun > 0) %>%
ggplot(aes(x=relabun, y=phylum, group=phylum, color=phylum)) +
scale_color_manual(values=phylum_colors[-8]) +
geom_jitter(alpha=0.5, show.legend = FALSE) +
facet_grid(.~type)+
theme_minimal() +
labs(y="Family", x="Relative abundance", color="Phylum")
5.2.2 Per season
phylum_summary %>%
group_by(phylum) %>%
summarise(total_mean=mean(relabun*100, na.rm=T),
total_sd=sd(relabun*100, na.rm=T),
spring_mean=mean(relabun[season=="spring"]*100, na.rm=T),
spring_sd=sd(relabun[season=="spring"]*100, na.rm=T),
autumn_mean=mean(relabun[season=="autumn"]*100, na.rm=T),
autumn_sd=sd(relabun[season=="autumn"]*100, na.rm=T)) %>%
mutate(total=str_c(round(total_mean,2),"±",round(total_sd,2)),
spring=str_c(round(spring_mean,2),"±",round(spring_sd,2)),
autumn=str_c(round(autumn_mean,2),"±",round(autumn_sd,2))) %>%
arrange(-total_mean) %>%
dplyr::select(phylum,total,spring,autumn) %>%
tt()| phylum | total | spring | autumn |
|---|---|---|---|
| p__Bacteroidota | 53.53±20.47 | 49.04±16.42 | 55.93±22.09 |
| p__Bacillota_A | 15.07±11.48 | 17.89±9.58 | 13.56±12.18 |
| p__Pseudomonadota | 13.1±18.44 | 15.38±16.87 | 11.89±19.25 |
| p__Bacillota | 5.62±7.54 | 5.54±5.29 | 5.66±8.54 |
| p__Verrucomicrobiota | 4.16±5.07 | 5.09±5.05 | 3.67±5.05 |
| p__Desulfobacterota | 2.11±2.92 | 2.64±2.09 | 1.83±3.26 |
| p__Cyanobacteriota | 1.4±6.77 | 1.34±3.83 | 1.43±7.93 |
| p__Chloroflexota | 1.04±3.88 | 1.11±4.11 | 1±3.78 |
| p__Fusobacteriota | 0.52±1.23 | 0.31±0.53 | 0.62±1.47 |
| p__Myxococcota | 0.5±4.84 | 0±0 | 0.77±6 |
| p__Bacillota_C | 0.47±0.77 | 0.43±0.77 | 0.49±0.78 |
| p__Patescibacteria | 0.37±1.58 | 0±0 | 0.57±1.93 |
| p__Acidobacteriota | 0.34±1.44 | 0.39±1.58 | 0.31±1.37 |
| p__Deferribacterota | 0.31±0.9 | 0.21±0.23 | 0.36±1.11 |
| p__Bacillota_B | 0.24±0.36 | 0.29±0.34 | 0.22±0.37 |
| p__Desulfobacterota_F | 0.23±1.04 | 0.08±0.37 | 0.31±1.26 |
| p__Halobacteriota | 0.21±1.41 | 0.02±0.05 | 0.31±1.75 |
| p__Planctomycetota | 0.17±1.16 | 0±0 | 0.26±1.44 |
| p__Thermoproteota | 0.15±0.55 | 0.06±0.25 | 0.2±0.65 |
| p__Nanoarchaeota | 0.07±0.65 | 0±0 | 0.11±0.81 |
| p__Spirochaetota | 0.07±0.31 | 0.13±0.43 | 0.04±0.22 |
| p__Campylobacterota | 0.06±0.3 | 0.04±0.13 | 0.08±0.36 |
| p__Methanobacteriota | 0.04±0.28 | 0.03±0.11 | 0.05±0.34 |
| p__Actinomycetota | 0.04±0.2 | 0±0 | 0.06±0.24 |
| p__Fibrobacterota | 0.04±0.35 | 0±0 | 0.06±0.43 |
| p__ | 0.04±0.29 | 0±0 | 0.05±0.36 |
| p__Chlamydiota | 0.03±0.14 | 0±0 | 0.04±0.18 |
| p__Desulfobacterota_G | 0.03±0.2 | 0±0 | 0.04±0.25 |
| p__J088 | 0.02±0.11 | 0±0 | 0.03±0.14 |
| p__Iainarchaeota | 0.01±0.1 | 0±0 | 0.02±0.12 |
| p__JAKLEM01 | 0.01±0.11 | 0±0 | 0.02±0.14 |
| p__Omnitrophota | 0.01±0.05 | 0±0 | 0.01±0.06 |
phylum_summary %>%
filter(phylum %in% phylum_arrange) %>%
mutate(phylum=factor(phylum,levels=rev(phylum_arrange))) %>%
filter(relabun > 0) %>%
ggplot(aes(x=relabun, y=phylum, group=phylum, color=phylum)) +
scale_color_manual(values=phylum_colors[-8]) +
geom_jitter(alpha=0.5, show.legend = FALSE) +
facet_grid(.~season)+
theme_minimal() +
labs(y="Family", x="Relative abundance", color="Phylum")
5.3 Family relative abundances
family_summary <- genome_counts_filt %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(sample_metadata, by = join_by(sample == sample)) %>% #append sample metadata
left_join(., genome_metadata, by = join_by(genome == genome)) %>% #append genome metadata
group_by(sample,family, type, region, season) %>%
summarise(relabun=sum(count))
family_arrange <- family_summary %>%
group_by(family) %>%
summarise(mean=sum(relabun)) %>%
arrange(-mean) %>%
select(family) %>%
pull()
family_summary %>%
left_join(genome_metadata %>% dplyr::select(family,phylum) %>% unique(),by=join_by(family==family)) %>%
# left_join(sample_metadata,by=join_by(sample==sample)) %>%
filter(family %in% family_arrange[1:20]) %>%
mutate(family=factor(family,levels=rev(family_arrange[1:20]))) %>%
filter(relabun > 0) %>%
ggplot(aes(x=relabun, y=family, group=family, color=phylum)) +
scale_color_manual(values=phylum_colors) +
geom_jitter(alpha=0.5) +
theme_minimal() +
labs(y="Family", x="Relative abundance", color="Phylum")
5.3.1 Per pond
family_summary %>%
group_by(family) %>%
summarise(total_mean=mean(relabun*100, na.rm=T),
total_sd=sd(relabun*100, na.rm=T),
natural_mean=mean(relabun[type=="natural"]*100, na.rm=T),
natural_sd=sd(relabun[type=="natural"]*100, na.rm=T),
protected_mean=mean(relabun[type=="protected"]*100, na.rm=T),
protected_sd=sd(relabun[type=="protected"]*100, na.rm=T),
urban_mean=mean(relabun[type=="urban"]*100, na.rm=T),
urban_sd=sd(relabun[type=="urban"]*100, na.rm=T)) %>%
mutate(total=str_c(round(total_mean,2),"±",round(total_sd,2)),
natural=str_c(round(natural_mean,2),"±",round(natural_sd,2)),
protected=str_c(round(protected_mean,2),"±",round(protected_sd,2)),
urban=str_c(round(urban_mean,2),"±",round(urban_sd,2))) %>%
arrange(-total_mean) %>%
dplyr::select(family,total,natural,protected,urban) %>%
tt()| family | total | natural | protected | urban |
|---|---|---|---|---|
| f__Rikenellaceae | 19.24±15.88 | 21.56±16 | 16.39±18.36 | 18.8±11.83 |
| f__Bacteroidaceae | 17.76±15.59 | 13.58±15.39 | 24.32±16.86 | 16.77±11.57 |
| f__Tannerellaceae | 8.3±7.4 | 5.02±6.44 | 11.2±8.17 | 10.33±5.71 |
| f__Lachnospiraceae | 4.6±4.74 | 2.96±3.69 | 6.66±6.02 | 4.87±3.47 |
| f__Mycoplasmoidaceae | 4.22±6.93 | 5.61±8.92 | 2.78±4.29 | 3.63±5.26 |
| f__Aeromonadaceae | 4.15±10.69 | 3.35±9.89 | 4.22±9.85 | 5.47±13.15 |
| f__Ruminococcaceae | 4.08±3.91 | 4.28±4.41 | 3.9±3.98 | 3.97±2.91 |
| f__Marinifilaceae | 3±3.32 | 1.91±2.49 | 3.93±4.15 | 3.73±2.97 |
| f__Akkermansiaceae | 2.9±4.04 | 2.81±3.77 | 2.97±4.33 | 2.97±4.31 |
| f__Enterobacteriaceae | 2.67±6.28 | 2.28±5.65 | 3.73±8.03 | 2.03±4.75 |
| f__ | 2.22±2.48 | 2.37±2.89 | 2.02±2.22 | 2.21±2.06 |
| f__Clostridiaceae | 2.14±3.23 | 1.67±1.76 | 2.37±5 | 2.65±2.24 |
| f__Desulfovibrionaceae | 1.73±1.88 | 1.49±1.68 | 1.51±1.92 | 2.44±2.03 |
| f__Chlorobiaceae | 1.52±9.28 | 3.48±13.92 | 0±0 | 0.02±0.07 |
| f__Chromatiaceae | 1.33±5.58 | 2.36±7.66 | 0.76±4.07 | 0.27±0.66 |
| f__Butyricicoccaceae | 1.32±5.64 | 0.44±0.85 | 3.28±9.8 | 0.39±0.86 |
| f__Erysipelotrichaceae | 1.25±2.02 | 1.62±2.77 | 0.87±1.09 | 1.08±1.15 |
| f__Diplorickettsiaceae | 0.99±8.81 | 2.21±13.36 | 0.03±0.11 | 0.08±0.25 |
| f__Cellulosilyticaceae | 0.69±1.35 | 0.42±0.72 | 0.34±0.73 | 1.59±2.2 |
| f__FACHB-T130 | 0.68±6.41 | 1.57±9.72 | 0±0 | 0±0 |
| f__CAG-239 | 0.64±1.08 | 0.33±0.46 | 0.89±1.55 | 0.86±1.04 |
| f__VadinHA17 | 0.55±1.87 | 0.99±2.41 | 0±0 | 0.48±1.85 |
| f__Methylococcaceae | 0.55±3.81 | 1.26±5.75 | 0±0 | 0±0 |
| f__Fusobacteriaceae | 0.52±1.23 | 0.26±0.51 | 0.45±1.36 | 1.05±1.74 |
| f__Polyangiaceae | 0.5±4.84 | 0±0 | 0±0 | 2.02±9.68 |
| f__EnvOPS12 | 0.47±1.77 | 0.71±1.82 | 0.09±0.48 | 0.53±2.55 |
| f__Oscillospiraceae | 0.41±0.45 | 0.28±0.36 | 0.6±0.56 | 0.4±0.34 |
| f__Rhodocyclaceae | 0.41±2.05 | 0.88±3.06 | 0±0 | 0.09±0.2 |
| f__Gastranaerophilaceae | 0.39±0.67 | 0.3±0.62 | 0.31±0.56 | 0.64±0.81 |
| f__Anaerovoracaceae | 0.37±0.46 | 0.39±0.54 | 0.25±0.32 | 0.48±0.44 |
| f__Pumilibacteraceae | 0.34±1.11 | 0.57±1.61 | 0.15±0.22 | 0.2±0.5 |
| f__P3 | 0.34±0.64 | 0.36±0.53 | 0.27±0.67 | 0.39±0.78 |
| f__UBA1997 | 0.34±0.81 | 0.32±0.72 | 0.1±0.3 | 0.67±1.2 |
| f__Mucispirillaceae | 0.31±0.9 | 0.52±1.33 | 0.12±0.21 | 0.17±0.24 |
| f__CAIVKH01 | 0.3±2.01 | 0.69±3.03 | 0±0 | 0±0 |
| f__UBA3637 | 0.3±0.65 | 0.18±0.52 | 0.36±0.74 | 0.45±0.74 |
| f__UBA11358 | 0.28±1.11 | 0.65±1.62 | 0±0 | 0±0 |
| f__Peptostreptococcaceae | 0.26±0.66 | 0.3±0.51 | 0.33±1 | 0.1±0.17 |
| f__Burkholderiaceae_B | 0.26±1.3 | 0.3±1.53 | 0±0 | 0.52±1.65 |
| f__Methylomonadaceae | 0.25±1.68 | 0.57±2.53 | 0±0.01 | 0±0 |
| f__Competibacteraceae | 0.25±2.33 | 0.01±0.05 | 0.77±4.15 | 0.01±0.04 |
| f__Chitinophagaceae | 0.25±1.22 | 0.57±1.81 | 0±0 | 0.01±0.03 |
| f__Peptococcaceae | 0.24±0.36 | 0.08±0.22 | 0.32±0.31 | 0.43±0.48 |
| f__CHK158-818 | 0.23±0.4 | 0.13±0.3 | 0.18±0.26 | 0.47±0.58 |
| f__Muribaculaceae | 0.22±0.37 | 0.31±0.45 | 0.1±0.22 | 0.23±0.32 |
| f__SHND01 | 0.21±1.4 | 0.48±2.1 | 0±0 | 0±0 |
| f__Chromobacteriaceae | 0.2±1.39 | 0.44±2.1 | 0±0 | 0.04±0.12 |
| f__Smithellaceae | 0.19±1.78 | 0±0 | 0±0 | 0.78±3.55 |
| f__Chloroflexaceae | 0.19±1.8 | 0±0 | 0.6±3.21 | 0±0 |
| f__UBA6186 | 0.17±1.46 | 0±0 | 0.51±2.59 | 0.03±0.12 |
| f__Pseudopelobacteraceae | 0.17±0.98 | 0.38±1.46 | 0±0 | 0±0 |
| f__Microcystaceae_B | 0.17±1.54 | 0.01±0.05 | 0.51±2.74 | 0±0 |
| f__Saprospiraceae | 0.16±0.89 | 0.37±1.33 | 0±0 | 0±0 |
| f__Succinispiraceae | 0.14±0.24 | 0.17±0.27 | 0.04±0.11 | 0.22±0.26 |
| f__Anaerotignaceae | 0.14±0.24 | 0.12±0.26 | 0.14±0.21 | 0.18±0.22 |
| f__Prolixibacteraceae | 0.14±0.71 | 0.16±0.5 | 0±0 | 0.26±1.26 |
| f__Palsa-965 | 0.13±0.89 | 0.3±1.33 | 0±0 | 0±0 |
| f__UBA4823 | 0.13±1.22 | 0±0 | 0±0 | 0.51±2.44 |
| f__Opitutaceae | 0.13±1.2 | 0±0 | 0±0 | 0.5±2.41 |
| f__Microcoleaceae | 0.12±0.81 | 0.09±0.48 | 0.26±1.33 | 0±0 |
| f__UBA3700 | 0.12±0.44 | 0.08±0.21 | 0.19±0.71 | 0.11±0.24 |
| f__B-1AR | 0.12±0.81 | 0.1±0.56 | 0±0 | 0.3±1.44 |
| f__Massilibacillaceae | 0.12±0.56 | 0±0 | 0.34±0.97 | 0.04±0.16 |
| f__UBA5066 | 0.11±0.78 | 0.26±1.17 | 0±0 | 0±0 |
| f__HGW-15 | 0.1±0.78 | 0±0 | 0±0 | 0.41±1.55 |
| f__UBA5704 | 0.1±0.96 | 0.23±1.45 | 0±0 | 0±0 |
| f__Planctomycetaceae | 0.1±0.94 | 0.23±1.43 | 0±0 | 0±0 |
| f__Methanoregulaceae | 0.09±0.74 | 0.03±0.19 | 0±0 | 0.3±1.45 |
| f__Staskawiczbacteraceae | 0.09±0.77 | 0.2±1.17 | 0±0 | 0±0 |
| f__B-17BO | 0.08±0.54 | 0.19±0.82 | 0±0 | 0±0 |
| f__CAG-465 | 0.07±0.36 | 0±0 | 0.17±0.59 | 0.09±0.25 |
| f__Paludibacteraceae | 0.07±0.56 | 0.04±0.25 | 0±0 | 0.23±1.07 |
| f__GW2011-AR1 | 0.07±0.65 | 0.17±0.99 | 0±0 | 0±0 |
| f__UBA10030 | 0.07±0.42 | 0.17±0.62 | 0±0 | 0±0 |
| f__Methanotrichaceae | 0.07±0.68 | 0±0 | 0±0 | 0.29±1.35 |
| f__UBA932 | 0.07±0.19 | 0.03±0.11 | 0.08±0.23 | 0.13±0.24 |
| f__Ignavibacteriaceae | 0.07±0.58 | 0.16±0.88 | 0±0 | 0±0 |
| f__Acutalibacteraceae | 0.07±0.39 | 0.13±0.58 | 0.03±0.13 | 0±0 |
| f__CAIRTM01 | 0.06±0.39 | 0.15±0.59 | 0±0 | 0±0 |
| f__OLB5 | 0.06±0.35 | 0.14±0.52 | 0±0 | 0±0 |
| f__Beijerinckiaceae | 0.06±0.28 | 0.14±0.42 | 0±0 | 0±0 |
| f__Victivallaceae | 0.06±0.28 | 0.02±0.06 | 0±0 | 0.2±0.54 |
| f__UBA4417 | 0.06±0.33 | 0.13±0.5 | 0±0 | 0±0 |
| f__Methylophilaceae | 0.06±0.29 | 0.11±0.43 | 0±0 | 0.03±0.08 |
| f__UBA3830 | 0.06±0.15 | 0.04±0.08 | 0.02±0.08 | 0.13±0.26 |
| f__UBA12108 | 0.05±0.43 | 0.12±0.65 | 0±0 | 0±0 |
| f__TH1-2 | 0.05±0.31 | 0.11±0.47 | 0±0 | 0±0 |
| f__Shewanellaceae | 0.05±0.22 | 0.03±0.2 | 0.09±0.3 | 0.02±0.07 |
| f__F082 | 0.05±0.37 | 0.11±0.57 | 0±0 | 0±0 |
| f__Arcobacteraceae | 0.05±0.28 | 0.1±0.43 | 0.01±0.03 | 0±0.01 |
| f__WRBN01 | 0.04±0.26 | 0.01±0.04 | 0±0 | 0.17±0.51 |
| f__Methanocorpusculaceae | 0.04±0.16 | 0.06±0.2 | 0.04±0.18 | 0.03±0.06 |
| f__Acidobacteriaceae | 0.04±0.41 | 0±0 | 0±0 | 0.17±0.82 |
| f__Hepatoplasmataceae | 0.04±0.29 | 0.04±0.26 | 0±0 | 0.1±0.48 |
| f__Methanobacteriaceae | 0.04±0.28 | 0.09±0.42 | 0±0 | 0.01±0.05 |
| f__UBA660 | 0.04±0.23 | 0.04±0.26 | 0.07±0.29 | 0±0.02 |
| f__DYRC01 | 0.04±0.39 | 0±0 | 0±0 | 0.16±0.79 |
| f__RUG14156 | 0.04±0.23 | 0.06±0.33 | 0±0 | 0.05±0.14 |
| f__JADJPG01 | 0.04±0.27 | 0.09±0.41 | 0±0 | 0±0 |
| f__SZUA-47 | 0.04±0.22 | 0.09±0.33 | 0±0 | 0±0 |
| f__Pyrinomonadaceae | 0.04±0.24 | 0.09±0.37 | 0±0 | 0±0 |
| f__LL51 | 0.04±0.17 | 0.01±0.05 | 0.1±0.29 | 0±0 |
| f__Pirellulaceae | 0.04±0.29 | 0.08±0.44 | 0±0 | 0±0 |
| f__FEN-979 | 0.04±0.21 | 0.08±0.31 | 0±0 | 0±0 |
| f__UBA9973 | 0.03±0.15 | 0.05±0.18 | 0±0 | 0.04±0.18 |
| f__Rhizobiaceae | 0.03±0.15 | 0.07±0.22 | 0±0 | 0±0 |
| f__SHXO01 | 0.03±0.14 | 0.07±0.21 | 0±0 | 0±0 |
| f__Rhabdochlamydiaceae | 0.03±0.14 | 0.06±0.21 | 0±0 | 0±0 |
| f__2-12-FULL-35-15 | 0.03±0.22 | 0.06±0.33 | 0±0 | 0±0 |
| f__Aestuariivirgaceae | 0.03±0.11 | 0.06±0.17 | 0±0 | 0±0 |
| f__Syntrophorhabdaceae | 0.03±0.2 | 0.01±0.08 | 0±0 | 0.08±0.39 |
| f__Sedimentibacteraceae | 0.03±0.07 | 0.01±0.03 | 0.06±0.11 | 0.02±0.07 |
| f__UBA2023 | 0.02±0.2 | 0.06±0.31 | 0±0 | 0±0 |
| f__Coprobacillaceae | 0.02±0.07 | 0.03±0.06 | 0.03±0.1 | 0±0.01 |
| f__Spirosomaceae | 0.02±0.12 | 0.03±0.15 | 0.03±0.11 | 0±0 |
| f__UBA3375 | 0.02±0.11 | 0.05±0.16 | 0±0 | 0.01±0.02 |
| f__Sphingomonadaceae | 0.02±0.11 | 0.05±0.16 | 0±0 | 0±0 |
| f__Thermoanaerobaculaceae | 0.02±0.22 | 0±0 | 0±0 | 0.09±0.43 |
| f__Fen-1058 | 0.02±0.2 | 0±0 | 0±0 | 0.09±0.39 |
| f__DUVY01 | 0.02±0.06 | 0.02±0.05 | 0.03±0.08 | 0.02±0.06 |
| f__UBA927 | 0.02±0.1 | 0.04±0.14 | 0±0 | 0.02±0.1 |
| f__JAAUTT01 | 0.02±0.12 | 0.05±0.17 | 0±0 | 0±0 |
| f__GWF2-50-10 | 0.02±0.13 | 0.05±0.2 | 0±0 | 0±0 |
| f__UBA3254 | 0.02±0.13 | 0.04±0.2 | 0±0 | 0±0 |
| f__GWA2-36-10 | 0.02±0.15 | 0.04±0.22 | 0±0 | 0±0 |
| f__JAAYKM01 | 0.02±0.18 | 0±0 | 0±0 | 0.08±0.36 |
| f__SG8-41 | 0.02±0.15 | 0.04±0.22 | 0±0 | 0±0 |
| f__Crocinitomicaceae | 0.02±0.12 | 0±0 | 0±0 | 0.07±0.24 |
| f__Holophagaceae | 0.02±0.18 | 0±0 | 0±0 | 0.07±0.35 |
| f__Absconditicoccaceae | 0.02±0.15 | 0.04±0.23 | 0±0 | 0±0 |
| f__Rectinemataceae | 0.02±0.17 | 0±0 | 0±0 | 0.07±0.34 |
| f__Ilumatobacteraceae | 0.02±0.12 | 0.04±0.18 | 0±0 | 0±0 |
| f__UBA6016 | 0.02±0.11 | 0±0 | 0±0 | 0.07±0.21 |
| f__Lutisporaceae | 0.02±0.04 | 0.01±0.03 | 0.01±0.03 | 0.04±0.06 |
| f__4484-276 | 0.02±0.1 | 0.04±0.16 | 0±0 | 0±0 |
| f__Terrimicrobiaceae | 0.02±0.06 | 0.03±0.09 | 0±0 | 0±0.02 |
| f__UBA4778 | 0.02±0.09 | 0.02±0.08 | 0±0 | 0.03±0.14 |
| f__Eubacteriaceae | 0.02±0.05 | 0±0 | 0.02±0.04 | 0.04±0.09 |
| f__SPBP01 | 0.01±0.09 | 0.03±0.13 | 0±0 | 0±0 |
| f__Gemmataceae | 0.01±0.14 | 0.03±0.21 | 0±0 | 0±0 |
| f__UBA1568 | 0.01±0.1 | 0.03±0.16 | 0±0 | 0±0 |
| f__XYD1-FULL-46-19 | 0.01±0.11 | 0.03±0.16 | 0±0 | 0±0 |
| f__UBA920 | 0.01±0.1 | 0.03±0.15 | 0±0 | 0±0 |
| f__CAG-508 | 0.01±0.08 | 0.02±0.12 | 0±0.02 | 0.01±0.03 |
| f__Steroidobacteraceae | 0.01±0.08 | 0.03±0.11 | 0±0 | 0±0 |
| f__JAAZKV01 | 0.01±0.1 | 0.03±0.15 | 0±0 | 0±0 |
| f__UBA5976 | 0.01±0.08 | 0.03±0.11 | 0±0 | 0±0.02 |
| f__Burkholderiaceae_A | 0.01±0.09 | 0.03±0.14 | 0±0 | 0±0 |
| f__JAKLEM01 | 0.01±0.11 | 0±0 | 0±0 | 0.05±0.22 |
| f__Brevinemataceae | 0.01±0.07 | 0.01±0.06 | 0.02±0.09 | 0±0 |
| f__Amoebophilaceae | 0.01±0.05 | 0.02±0.07 | 0±0 | 0±0 |
| f__Profunditerraquicolaceae | 0.01±0.05 | 0.02±0.07 | 0±0 | 0±0 |
| f__JAGOQP01 | 0.01±0.09 | 0±0 | 0±0 | 0.04±0.17 |
| f__Mycoplasmataceae | 0.01±0.06 | 0±0 | 0±0 | 0.04±0.11 |
| f__Microbacteriaceae | 0.01±0.06 | 0.02±0.08 | 0±0 | 0±0.01 |
| f__UBA1709 | 0.01±0.08 | 0.02±0.12 | 0±0 | 0±0 |
| f__UBA1820 | 0.01±0.02 | 0.01±0.02 | 0.01±0.02 | 0.01±0.02 |
| f__Burkholderiaceae | 0.01±0.03 | 0.01±0.04 | 0±0 | 0±0.01 |
| f__JAGQMS01 | 0.01±0.03 | 0.02±0.05 | 0±0 | 0±0 |
| f__Tenuifilaceae | 0.01±0.05 | 0.01±0.07 | 0±0 | 0±0 |
| f__UBA5272 | 0.01±0.05 | 0.01±0.07 | 0±0 | 0±0 |
| f__Flavobacteriaceae | 0.01±0.05 | 0.01±0.07 | 0±0 | 0±0 |
| f__Moraxellaceae | 0±0.04 | 0±0 | 0.02±0.06 | 0±0 |
| f__Zambryskibacteraceae | 0±0.04 | 0.01±0.06 | 0±0 | 0±0 |
| f__JAFDDL01 | 0±0.04 | 0±0 | 0±0 | 0.02±0.09 |
| f__2-12-FULL-60-25 | 0±0.02 | 0.01±0.04 | 0±0 | 0±0 |
| f__UBA12049 | 0±0.03 | 0.01±0.04 | 0±0 | 0±0 |
| f__PALSA-1337 | 0±0.02 | 0.01±0.03 | 0±0 | 0±0 |
| f__CAIOMD01 | 0±0.01 | 0±0.02 | 0±0 | 0±0 |
family_arrange <- family_summary %>%
group_by(family) %>%
summarise(mean=sum(relabun)) %>%
arrange(-mean) %>%
dplyr::select(family) %>%
pull()
family_summary %>%
left_join(genome_metadata %>% dplyr::select(family,phylum) %>% unique(),by=join_by(family==family)) %>%
# left_join(sample_metadata,by=join_by(sample==sample)) %>%
filter(family %in% family_arrange[1:20]) %>%
mutate(family=factor(family,levels=rev(family_arrange[1:20]))) %>%
filter(relabun > 0) %>%
ggplot(aes(x=relabun, y=family, group=family, color=phylum)) +
scale_color_manual(values=phylum_colors) +
geom_jitter(alpha=0.5) +
facet_grid(.~type)+
theme_minimal() +
labs(y="Family", x="Relative abundance", color="Phylum")
# Per origin
# family_summary %>%
# left_join(genome_metadata %>% dplyr::select(family,phylum) %>% unique(),by=join_by(family==family)) %>%
# # left_join(sample_metadata,by=join_by(sample==sample)) %>%
# filter(family %in% family_arrange[1:20]) %>%
# mutate(family=factor(family,levels=rev(family_arrange[1:20]))) %>%
# filter(relabun > 0) %>%
# ggplot(aes(x=relabun, y=family, group=family, color=phylum)) +
# scale_color_manual(values=phylum_colors[-8]) +
# geom_jitter(alpha=0.5) +
# facet_grid(.~region)+
# theme_minimal() +
# labs(y="Family", x="Relative abundance", color="Phylum")5.3.2 Per season
family_summary %>%
group_by(family) %>%
summarise(total_mean=mean(relabun*100, na.rm=T),
total_sd=sd(relabun*100, na.rm=T),
spring_mean=mean(relabun[season=="spring"]*100, na.rm=T),
spring_sd=sd(relabun[season=="spring"]*100, na.rm=T),
autumn_mean=mean(relabun[season=="autumn"]*100, na.rm=T),
autumn_sd=sd(relabun[season=="autumn"]*100, na.rm=T)) %>%
mutate(total=str_c(round(total_mean,2),"±",round(total_sd,2)),
spring=str_c(round(spring_mean,2),"±",round(spring_sd,2)),
autumn=str_c(round(autumn_mean,2),"±",round(autumn_sd,2))) %>%
arrange(-total_mean) %>%
dplyr::select(family,total,spring,autumn) %>%
tt()| family | total | spring | autumn |
|---|---|---|---|
| f__Rikenellaceae | 19.24±15.88 | 21.24±11.62 | 18.17±17.74 |
| f__Bacteroidaceae | 17.76±15.59 | 12.4±8.63 | 20.62±17.65 |
| f__Tannerellaceae | 8.3±7.4 | 7.78±5.55 | 8.57±8.24 |
| f__Lachnospiraceae | 4.6±4.74 | 4.99±5.37 | 4.4±4.4 |
| f__Mycoplasmoidaceae | 4.22±6.93 | 4.36±4.98 | 4.15±7.82 |
| f__Aeromonadaceae | 4.15±10.69 | 4.36±9.73 | 4.04±11.25 |
| f__Ruminococcaceae | 4.08±3.91 | 6.17±4.42 | 2.97±3.11 |
| f__Marinifilaceae | 3±3.32 | 4.8±3.78 | 2.04±2.61 |
| f__Akkermansiaceae | 2.9±4.04 | 3.9±4.69 | 2.37±3.58 |
| f__Enterobacteriaceae | 2.67±6.28 | 3.18±7.34 | 2.4±5.69 |
| f__ | 2.22±2.48 | 2.83±2.55 | 1.89±2.4 |
| f__Clostridiaceae | 2.14±3.23 | 2.22±2.57 | 2.09±3.55 |
| f__Desulfovibrionaceae | 1.73±1.88 | 2.63±2.09 | 1.25±1.57 |
| f__Chlorobiaceae | 1.52±9.28 | 0±0 | 2.33±11.44 |
| f__Chromatiaceae | 1.33±5.58 | 2.04±6.47 | 0.95±5.07 |
| f__Butyricicoccaceae | 1.32±5.64 | 0.78±1.39 | 1.61±6.91 |
| f__Erysipelotrichaceae | 1.25±2.02 | 1.05±1.03 | 1.35±2.39 |
| f__Diplorickettsiaceae | 0.99±8.81 | 0±0 | 1.52±10.91 |
| f__Cellulosilyticaceae | 0.69±1.35 | 0.66±0.83 | 0.7±1.57 |
| f__FACHB-T130 | 0.68±6.41 | 0±0 | 1.05±7.94 |
| f__CAG-239 | 0.64±1.08 | 1.18±1.46 | 0.35±0.66 |
| f__VadinHA17 | 0.55±1.87 | 0.03±0.17 | 0.83±2.27 |
| f__Methylococcaceae | 0.55±3.81 | 1.35±6.41 | 0.12±0.59 |
| f__Fusobacteriaceae | 0.52±1.23 | 0.31±0.53 | 0.62±1.47 |
| f__Polyangiaceae | 0.5±4.84 | 0±0 | 0.77±6 |
| f__EnvOPS12 | 0.47±1.77 | 0.08±0.46 | 0.67±2.14 |
| f__Oscillospiraceae | 0.41±0.45 | 0.59±0.47 | 0.32±0.41 |
| f__Rhodocyclaceae | 0.41±2.05 | 0.15±0.63 | 0.54±2.5 |
| f__Gastranaerophilaceae | 0.39±0.67 | 0.49±0.65 | 0.33±0.67 |
| f__Anaerovoracaceae | 0.37±0.46 | 0.45±0.49 | 0.32±0.44 |
| f__Pumilibacteraceae | 0.34±1.11 | 0.64±1.77 | 0.19±0.4 |
| f__P3 | 0.34±0.64 | 0.51±0.7 | 0.25±0.59 |
| f__UBA1997 | 0.34±0.81 | 0.31±0.64 | 0.35±0.89 |
| f__Mucispirillaceae | 0.31±0.9 | 0.21±0.23 | 0.36±1.11 |
| f__CAIVKH01 | 0.3±2.01 | 0±0 | 0.46±2.48 |
| f__UBA3637 | 0.3±0.65 | 0.68±0.92 | 0.1±0.32 |
| f__UBA11358 | 0.28±1.11 | 0.22±0.86 | 0.32±1.23 |
| f__Peptostreptococcaceae | 0.26±0.66 | 0.38±0.67 | 0.2±0.65 |
| f__Burkholderiaceae_B | 0.26±1.3 | 0.01±0.05 | 0.39±1.6 |
| f__Methylomonadaceae | 0.25±1.68 | 0±0 | 0.38±2.07 |
| f__Competibacteraceae | 0.25±2.33 | 0.71±3.95 | 0±0 |
| f__Chitinophagaceae | 0.25±1.22 | 0±0 | 0.38±1.49 |
| f__Peptococcaceae | 0.24±0.36 | 0.29±0.34 | 0.22±0.37 |
| f__CHK158-818 | 0.23±0.4 | 0.39±0.55 | 0.14±0.26 |
| f__Muribaculaceae | 0.22±0.37 | 0.46±0.48 | 0.1±0.21 |
| f__SHND01 | 0.21±1.4 | 0.48±2.27 | 0.06±0.48 |
| f__Chromobacteriaceae | 0.2±1.39 | 0.58±2.34 | 0±0 |
| f__Smithellaceae | 0.19±1.78 | 0±0 | 0.3±2.2 |
| f__Chloroflexaceae | 0.19±1.8 | 0.54±3.06 | 0±0.01 |
| f__UBA6186 | 0.17±1.46 | 0.46±2.47 | 0.01±0.08 |
| f__Pseudopelobacteraceae | 0.17±0.98 | 0±0 | 0.25±1.2 |
| f__Microcystaceae_B | 0.17±1.54 | 0.46±2.6 | 0.01±0.04 |
| f__Saprospiraceae | 0.16±0.89 | 0±0 | 0.25±1.09 |
| f__Succinispiraceae | 0.14±0.24 | 0.12±0.17 | 0.15±0.27 |
| f__Anaerotignaceae | 0.14±0.24 | 0.15±0.23 | 0.13±0.24 |
| f__Prolixibacteraceae | 0.14±0.71 | 0±0 | 0.21±0.87 |
| f__Palsa-965 | 0.13±0.89 | 0±0 | 0.2±1.09 |
| f__UBA4823 | 0.13±1.22 | 0±0 | 0.19±1.51 |
| f__Opitutaceae | 0.13±1.2 | 0±0 | 0.19±1.49 |
| f__Microcoleaceae | 0.12±0.81 | 0.35±1.35 | 0±0.01 |
| f__UBA3700 | 0.12±0.44 | 0.21±0.68 | 0.07±0.2 |
| f__B-1AR | 0.12±0.81 | 0±0 | 0.18±0.99 |
| f__Massilibacillaceae | 0.12±0.56 | 0.16±0.78 | 0.09±0.42 |
| f__UBA5066 | 0.11±0.78 | 0.3±1.3 | 0.02±0.13 |
| f__HGW-15 | 0.1±0.78 | 0±0 | 0.16±0.96 |
| f__UBA5704 | 0.1±0.96 | 0±0 | 0.15±1.19 |
| f__Planctomycetaceae | 0.1±0.94 | 0±0 | 0.15±1.17 |
| f__Methanoregulaceae | 0.09±0.74 | 0±0 | 0.14±0.91 |
| f__Staskawiczbacteraceae | 0.09±0.77 | 0±0 | 0.13±0.95 |
| f__B-17BO | 0.08±0.54 | 0±0 | 0.13±0.67 |
| f__CAG-465 | 0.07±0.36 | 0.19±0.58 | 0.01±0.07 |
| f__Paludibacteraceae | 0.07±0.56 | 0±0 | 0.11±0.69 |
| f__GW2011-AR1 | 0.07±0.65 | 0±0 | 0.11±0.81 |
| f__UBA10030 | 0.07±0.42 | 0±0 | 0.11±0.51 |
| f__Methanotrichaceae | 0.07±0.68 | 0±0 | 0.11±0.84 |
| f__UBA932 | 0.07±0.19 | 0.12±0.24 | 0.04±0.16 |
| f__Ignavibacteriaceae | 0.07±0.58 | 0.02±0.12 | 0.09±0.72 |
| f__Acutalibacteraceae | 0.07±0.39 | 0.07±0.19 | 0.06±0.47 |
| f__CAIRTM01 | 0.06±0.39 | 0.08±0.37 | 0.06±0.41 |
| f__OLB5 | 0.06±0.35 | 0±0 | 0.1±0.43 |
| f__Beijerinckiaceae | 0.06±0.28 | 0±0 | 0.1±0.35 |
| f__Victivallaceae | 0.06±0.28 | 0.02±0.07 | 0.08±0.34 |
| f__UBA4417 | 0.06±0.33 | 0.02±0.11 | 0.07±0.41 |
| f__Methylophilaceae | 0.06±0.29 | 0±0 | 0.09±0.35 |
| f__UBA3830 | 0.06±0.15 | 0.06±0.13 | 0.06±0.16 |
| f__UBA12108 | 0.05±0.43 | 0±0 | 0.08±0.53 |
| f__TH1-2 | 0.05±0.31 | 0±0 | 0.08±0.38 |
| f__Shewanellaceae | 0.05±0.22 | 0±0 | 0.07±0.26 |
| f__F082 | 0.05±0.37 | 0.03±0.11 | 0.06±0.46 |
| f__Arcobacteraceae | 0.05±0.28 | 0.04±0.13 | 0.05±0.34 |
| f__WRBN01 | 0.04±0.26 | 0.12±0.43 | 0±0.03 |
| f__Methanocorpusculaceae | 0.04±0.16 | 0.02±0.05 | 0.06±0.2 |
| f__Acidobacteriaceae | 0.04±0.41 | 0±0 | 0.07±0.51 |
| f__Hepatoplasmataceae | 0.04±0.29 | 0±0 | 0.07±0.36 |
| f__Methanobacteriaceae | 0.04±0.28 | 0.03±0.11 | 0.05±0.34 |
| f__UBA660 | 0.04±0.23 | 0.12±0.39 | 0±0.01 |
| f__DYRC01 | 0.04±0.39 | 0±0 | 0.06±0.49 |
| f__RUG14156 | 0.04±0.23 | 0.03±0.12 | 0.04±0.27 |
| f__JADJPG01 | 0.04±0.27 | 0±0 | 0.06±0.33 |
| f__SZUA-47 | 0.04±0.22 | 0±0 | 0.06±0.27 |
| f__Pyrinomonadaceae | 0.04±0.24 | 0.09±0.4 | 0.01±0.07 |
| f__LL51 | 0.04±0.17 | 0.08±0.27 | 0.01±0.05 |
| f__Pirellulaceae | 0.04±0.29 | 0±0 | 0.06±0.36 |
| f__FEN-979 | 0.04±0.21 | 0±0 | 0.06±0.25 |
| f__UBA9973 | 0.03±0.15 | 0±0 | 0.05±0.19 |
| f__Rhizobiaceae | 0.03±0.15 | 0±0 | 0.05±0.18 |
| f__SHXO01 | 0.03±0.14 | 0±0 | 0.04±0.18 |
| f__Rhabdochlamydiaceae | 0.03±0.14 | 0±0 | 0.04±0.18 |
| f__2-12-FULL-35-15 | 0.03±0.22 | 0±0 | 0.04±0.27 |
| f__Aestuariivirgaceae | 0.03±0.11 | 0±0 | 0.04±0.14 |
| f__Syntrophorhabdaceae | 0.03±0.2 | 0±0 | 0.04±0.25 |
| f__Sedimentibacteraceae | 0.03±0.07 | 0.02±0.07 | 0.03±0.07 |
| f__UBA2023 | 0.02±0.2 | 0±0 | 0.04±0.25 |
| f__Coprobacillaceae | 0.02±0.07 | 0.01±0.04 | 0.03±0.08 |
| f__Spirosomaceae | 0.02±0.12 | 0.02±0.1 | 0.03±0.13 |
| f__UBA3375 | 0.02±0.11 | 0±0 | 0.04±0.13 |
| f__Sphingomonadaceae | 0.02±0.11 | 0±0 | 0.04±0.13 |
| f__Thermoanaerobaculaceae | 0.02±0.22 | 0±0 | 0.03±0.27 |
| f__Fen-1058 | 0.02±0.2 | 0±0 | 0.03±0.24 |
| f__DUVY01 | 0.02±0.06 | 0.01±0.05 | 0.03±0.07 |
| f__UBA927 | 0.02±0.1 | 0±0 | 0.03±0.13 |
| f__JAAUTT01 | 0.02±0.12 | 0±0 | 0.03±0.14 |
| f__GWF2-50-10 | 0.02±0.13 | 0±0 | 0.03±0.16 |
| f__UBA3254 | 0.02±0.13 | 0±0 | 0.03±0.16 |
| f__GWA2-36-10 | 0.02±0.15 | 0±0 | 0.03±0.18 |
| f__JAAYKM01 | 0.02±0.18 | 0±0 | 0.03±0.23 |
| f__SG8-41 | 0.02±0.15 | 0±0 | 0.03±0.18 |
| f__Crocinitomicaceae | 0.02±0.12 | 0±0 | 0.03±0.15 |
| f__Holophagaceae | 0.02±0.18 | 0±0 | 0.03±0.22 |
| f__Absconditicoccaceae | 0.02±0.15 | 0±0 | 0.03±0.19 |
| f__Rectinemataceae | 0.02±0.17 | 0±0 | 0.03±0.21 |
| f__Ilumatobacteraceae | 0.02±0.12 | 0±0 | 0.03±0.15 |
| f__UBA6016 | 0.02±0.11 | 0±0 | 0.03±0.13 |
| f__Lutisporaceae | 0.02±0.04 | 0.03±0.05 | 0.01±0.03 |
| f__4484-276 | 0.02±0.1 | 0±0 | 0.03±0.13 |
| f__Terrimicrobiaceae | 0.02±0.06 | 0±0.02 | 0.02±0.07 |
| f__UBA4778 | 0.02±0.09 | 0.01±0.03 | 0.02±0.1 |
| f__Eubacteriaceae | 0.02±0.05 | 0.03±0.07 | 0.01±0.03 |
| f__SPBP01 | 0.01±0.09 | 0±0 | 0.02±0.11 |
| f__Gemmataceae | 0.01±0.14 | 0±0 | 0.02±0.17 |
| f__UBA1568 | 0.01±0.1 | 0±0 | 0.02±0.13 |
| f__XYD1-FULL-46-19 | 0.01±0.11 | 0±0 | 0.02±0.13 |
| f__UBA920 | 0.01±0.1 | 0±0 | 0.02±0.12 |
| f__CAG-508 | 0.01±0.08 | 0.03±0.13 | 0±0.02 |
| f__Steroidobacteraceae | 0.01±0.08 | 0±0 | 0.02±0.09 |
| f__JAAZKV01 | 0.01±0.1 | 0±0 | 0.02±0.12 |
| f__UBA5976 | 0.01±0.08 | 0±0 | 0.02±0.09 |
| f__Burkholderiaceae_A | 0.01±0.09 | 0.03±0.16 | 0±0 |
| f__JAKLEM01 | 0.01±0.11 | 0±0 | 0.02±0.14 |
| f__Brevinemataceae | 0.01±0.07 | 0.01±0.04 | 0.01±0.08 |
| f__Amoebophilaceae | 0.01±0.05 | 0±0 | 0.01±0.06 |
| f__Profunditerraquicolaceae | 0.01±0.05 | 0±0 | 0.01±0.06 |
| f__JAGOQP01 | 0.01±0.09 | 0±0 | 0.01±0.11 |
| f__Mycoplasmataceae | 0.01±0.06 | 0±0.01 | 0.01±0.07 |
| f__Microbacteriaceae | 0.01±0.06 | 0±0 | 0.01±0.07 |
| f__UBA1709 | 0.01±0.08 | 0±0 | 0.01±0.1 |
| f__UBA1820 | 0.01±0.02 | 0.01±0.02 | 0.01±0.02 |
| f__Burkholderiaceae | 0.01±0.03 | 0±0 | 0.01±0.04 |
| f__JAGQMS01 | 0.01±0.03 | 0±0 | 0.01±0.04 |
| f__Tenuifilaceae | 0.01±0.05 | 0±0 | 0.01±0.06 |
| f__UBA5272 | 0.01±0.05 | 0±0 | 0.01±0.06 |
| f__Flavobacteriaceae | 0.01±0.05 | 0±0 | 0.01±0.06 |
| f__Moraxellaceae | 0±0.04 | 0±0 | 0.01±0.04 |
| f__Zambryskibacteraceae | 0±0.04 | 0±0 | 0.01±0.05 |
| f__JAFDDL01 | 0±0.04 | 0±0 | 0.01±0.05 |
| f__2-12-FULL-60-25 | 0±0.02 | 0±0 | 0.01±0.03 |
| f__UBA12049 | 0±0.03 | 0±0 | 0.01±0.04 |
| f__PALSA-1337 | 0±0.02 | 0±0 | 0±0.02 |
| f__CAIOMD01 | 0±0.01 | 0±0 | 0±0.02 |
family_summary %>%
left_join(genome_metadata %>% dplyr::select(family,phylum) %>% unique(),by=join_by(family==family)) %>%
# left_join(sample_metadata,by=join_by(sample==sample)) %>%
filter(family %in% family_arrange[1:20]) %>%
mutate(family=factor(family,levels=rev(family_arrange[1:20]))) %>%
filter(relabun > 0) %>%
ggplot(aes(x=relabun, y=family, group=family, color=phylum)) +
scale_color_manual(values=phylum_colors) +#[-8]
geom_jitter(alpha=0.5) +
facet_grid(.~season)+
theme_minimal() +
labs(y="Family", x="Relative abundance", color="Phylum")
5.4 Genus relative abundances
genus_summary <- genome_counts_filt %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(sample_metadata, by = join_by(sample == sample)) %>% #append sample metadata
left_join(genome_metadata, by = join_by(genome == genome)) %>% #append genome metadata
group_by(sample,phylum,genus, type, season) %>%
summarise(relabun=sum(count)) %>%
filter(genus != "g__") %>%
mutate(genus= sub("^g__", "", genus))5.4.1 Per pond
genus_summary %>%
group_by(genus) %>%
summarise(total_mean=mean(relabun*100, na.rm=T),
total_sd=sd(relabun*100, na.rm=T),
natural_mean=mean(relabun[type=="natural"]*100, na.rm=T),
natural_sd=sd(relabun[type=="natural"]*100, na.rm=T),
protected_mean=mean(relabun[type=="protected"]*100, na.rm=T),
protected_sd=sd(relabun[type=="protected"]*100, na.rm=T),
urban_mean=mean(relabun[type=="urban"]*100, na.rm=T),
urban_sd=sd(relabun[type=="urban"]*100, na.rm=T)) %>%
mutate(total=str_c(round(total_mean,2),"±",round(total_sd,2)),
natural=str_c(round(natural_mean,2),"±",round(natural_sd,2)),
protected=str_c(round(protected_mean,2),"±",round(protected_sd,2)),
urban=str_c(round(urban_mean,2),"±",round(urban_sd,2))) %>%
arrange(-total_mean) %>%
dplyr::select(genus,total,natural,protected,urban) %>%
tt()| genus | total | natural | protected | urban |
|---|---|---|---|---|
| Bacteroides | 17.27±15.59 | 13.16±15.3 | 23.86±16.92 | 16.12±11.68 |
| Mucinivorans | 10.39±12.9 | 11.41±9.36 | 9.48±19.23 | 9.76±7.66 |
| Parabacteroides | 7.07±6.44 | 4.45±5.59 | 9.58±7.48 | 8.47±4.71 |
| Aeromonas | 4.15±10.69 | 3.35±9.89 | 4.22±9.85 | 5.47±13.15 |
| Mycoplasma_L | 3.78±6.81 | 5.42±8.83 | 2.17±4.18 | 2.96±4.7 |
| Rikenella | 2.79±5.08 | 3.21±5.27 | 2.46±4.91 | 2.48±5.12 |
| JADFUS01 | 2.22±2.02 | 2.13±2.26 | 2.31±2.09 | 2.27±1.5 |
| Odoribacter | 1.87±2.46 | 1.12±1.88 | 2.74±3.29 | 2.1±1.73 |
| Akkermansia | 1.63±3.1 | 0.86±1.42 | 2.06±3.58 | 2.41±4.22 |
| Clostridium | 1.41±1.84 | 1.53±1.71 | 1.3±2.38 | 1.33±1.22 |
| Chlorobaculum | 1.26±7.85 | 2.88±11.79 | 0±0 | 0.01±0.04 |
| UBA866 | 1.2±2.17 | 1.36±2.95 | 1.04±1.43 | 1.12±1.14 |
| Parabacteroides_B | 1.13±1.58 | 0.5±1.14 | 1.49±1.76 | 1.76±1.66 |
| Aquirickettsiella | 0.99±8.81 | 2.21±13.36 | 0.03±0.11 | 0.08±0.25 |
| Hafnia | 0.97±3.83 | 0.92±3.53 | 1.36±4.94 | 0.57±2.68 |
| Buttiauxella | 0.94±4.16 | 0.25±0.97 | 1.84±6.63 | 1.01±3.47 |
| Mobilisporobacter | 0.84±2.27 | 0.86±2.41 | 1.11±2.79 | 0.46±0.93 |
| Thiodictyon | 0.81±3.44 | 1.25±3.9 | 0.76±4.07 | 0.11±0.3 |
| UMGS1251 | 0.77±1.13 | 0.26±0.59 | 1.04±1.48 | 1.29±1.02 |
| Sarcina | 0.73±1.94 | 0.14±0.53 | 1.07±2.89 | 1.32±1.83 |
| Alistipes | 0.68±0.97 | 1.03±1.24 | 0.28±0.47 | 0.58±0.65 |
| FACHB-831 | 0.68±6.41 | 1.57±9.72 | 0±0 | 0±0 |
| Hydrogenoanaerobacterium | 0.66±1.76 | 0.89±2.49 | 0.45±0.81 | 0.53±0.89 |
| Clostridium_Q | 0.66±0.78 | 0.57±0.7 | 0.89±0.98 | 0.51±0.55 |
| SZUA-378 | 0.57±1.52 | 0.09±0.28 | 1.57±2.41 | 0.13±0.26 |
| Angelakisella | 0.56±0.72 | 0.56±0.73 | 0.4±0.69 | 0.77±0.74 |
| LD21 | 0.55±1.87 | 0.99±2.41 | 0±0 | 0.48±1.85 |
| Malacoplasma | 0.44±1.76 | 0.19±0.54 | 0.61±1.65 | 0.67±2.95 |
| Tidjanibacter | 0.41±0.75 | 0.51±0.85 | 0.34±0.79 | 0.34±0.49 |
| Hungatella_A | 0.4±0.64 | 0.29±0.56 | 0.42±0.68 | 0.57±0.71 |
| OLB14 | 0.39±1.69 | 0.59±1.67 | 0±0 | 0.53±2.55 |
| Budvicia | 0.38±1.36 | 0.41±1.55 | 0.45±1.48 | 0.23±0.8 |
| JAGNZR01 | 0.35±0.94 | 0.13±0.37 | 0.4±1.24 | 0.67±1.13 |
| Anaerorhabdus | 0.35±1.17 | 0.55±1.62 | 0.08±0.3 | 0.34±0.85 |
| Anaerotruncus | 0.31±0.48 | 0.27±0.47 | 0.35±0.56 | 0.35±0.41 |
| OM05-12 | 0.3±0.5 | 0.27±0.37 | 0.28±0.63 | 0.39±0.5 |
| CAIVKH01 | 0.3±2.01 | 0.69±3.03 | 0±0 | 0±0 |
| Chlorobium | 0.26±1.63 | 0.6±2.44 | 0±0 | 0.01±0.06 |
| RXIV01 | 0.25±2.33 | 0.01±0.05 | 0.77±4.15 | 0.01±0.04 |
| Gallalistipes | 0.25±0.71 | 0.44±1.03 | 0.07±0.14 | 0.12±0.14 |
| CAKVBE01 | 0.25±0.69 | 0.25±0.65 | 0.09±0.3 | 0.45±1.03 |
| Dielma | 0.23±0.36 | 0.15±0.32 | 0.26±0.36 | 0.34±0.39 |
| HGM05232 | 0.22±0.37 | 0.31±0.45 | 0.1±0.22 | 0.23±0.32 |
| SHND01 | 0.21±1.4 | 0.48±2.1 | 0±0 | 0±0 |
| Avirikenella | 0.2±0.64 | 0.33±0.91 | 0.1±0.3 | 0.12±0.3 |
| UBA4132 | 0.2±1.49 | 0.47±2.25 | 0±0.01 | 0±0 |
| Bilophila | 0.2±0.32 | 0.25±0.36 | 0.14±0.29 | 0.2±0.3 |
| Craterilacuibacter | 0.2±1.39 | 0.43±2.1 | 0±0 | 0.04±0.12 |
| Gallibacteroides | 0.2±0.38 | 0.11±0.27 | 0.12±0.2 | 0.44±0.57 |
| CAJGBR01 | 0.19±0.26 | 0.26±0.31 | 0.1±0.18 | 0.19±0.23 |
| Chloroploca | 0.19±1.8 | 0±0 | 0.6±3.21 | 0±0 |
| Lamprocystis | 0.18±0.88 | 0.35±1.3 | 0±0 | 0.12±0.28 |
| FEN-1139 | 0.18±1.71 | 0±0 | 0±0 | 0.71±3.43 |
| RUG14305 | 0.18±0.25 | 0.14±0.23 | 0.19±0.3 | 0.23±0.2 |
| Alistipes_A | 0.17±0.32 | 0.23±0.44 | 0.05±0.09 | 0.21±0.23 |
| Smithella | 0.17±1.55 | 0±0 | 0±0 | 0.68±3.09 |
| UBA6186 | 0.17±1.46 | 0±0 | 0.51±2.59 | 0.03±0.12 |
| Anaerovorax | 0.17±0.32 | 0.22±0.38 | 0.04±0.13 | 0.23±0.33 |
| Phocea | 0.16±0.35 | 0.06±0.12 | 0.22±0.53 | 0.27±0.31 |
| M3007 | 0.16±0.89 | 0.37±1.33 | 0±0 | 0±0 |
| Romboutsia_D | 0.16±0.34 | 0.26±0.39 | 0.09±0.36 | 0.07±0.15 |
| Cetobacterium | 0.16±0.45 | 0.12±0.31 | 0.04±0.15 | 0.38±0.74 |
| JADLHS01 | 0.16±0.93 | 0.36±1.39 | 0±0 | 0±0 |
| Scandinavium | 0.15±0.85 | 0.23±1.23 | 0.04±0.19 | 0.14±0.49 |
| Amedibacillus | 0.15±0.43 | 0.2±0.54 | 0.14±0.41 | 0.06±0.15 |
| JAGAJR01 | 0.14±0.29 | 0.15±0.29 | 0.12±0.26 | 0.17±0.31 |
| Luteolibacter | 0.14±0.53 | 0.32±0.78 | 0±0.01 | 0.02±0.07 |
| GCA-2737665 | 0.13±0.89 | 0.3±1.33 | 0±0 | 0±0 |
| Aminipila | 0.13±0.18 | 0.13±0.2 | 0.13±0.18 | 0.13±0.15 |
| CAIQJJ01 | 0.13±1.22 | 0±0 | 0±0 | 0.51±2.44 |
| JADKHC01 | 0.13±1.2 | 0±0 | 0±0 | 0.5±2.41 |
| JJ008 | 0.12±0.69 | 0.29±1.03 | 0±0 | 0±0 |
| Intestinimonas | 0.12±0.2 | 0.06±0.12 | 0.25±0.26 | 0.06±0.13 |
| Citrobacter | 0.12±1.12 | 0.28±1.69 | 0±0 | 0±0 |
| Planktothrix | 0.12±0.81 | 0.09±0.48 | 0.26±1.33 | 0±0 |
| FEN-1279 | 0.12±0.81 | 0.1±0.56 | 0±0 | 0.3±1.44 |
| Harryflintia | 0.12±0.32 | 0.02±0.12 | 0.28±0.5 | 0.06±0.12 |
| UBA5066 | 0.11±0.78 | 0.26±1.17 | 0±0 | 0±0 |
| JACRCG01 | 0.11±0.7 | 0.26±1.05 | 0±0 | 0±0 |
| Negativibacillus | 0.11±0.35 | 0.03±0.19 | 0.21±0.51 | 0.13±0.3 |
| Rhodoferax_C | 0.11±0.86 | 0.25±1.3 | 0±0 | 0±0 |
| CAIPUE01 | 0.11±0.28 | 0.13±0.35 | 0.09±0.24 | 0.09±0.19 |
| WRKB01 | 0.11±0.21 | 0.05±0.11 | 0.12±0.24 | 0.19±0.28 |
| Anaerotignum | 0.1±0.23 | 0.12±0.26 | 0.04±0.15 | 0.16±0.23 |
| Spyradomonas | 0.1±0.3 | 0.06±0.24 | 0.03±0.11 | 0.25±0.47 |
| TH-plancto1 | 0.1±0.94 | 0.23±1.43 | 0±0 | 0±0 |
| Azonexus | 0.09±0.43 | 0.17±0.63 | 0±0 | 0.07±0.2 |
| Methanoregula | 0.09±0.74 | 0.03±0.19 | 0±0 | 0.3±1.45 |
| Pseudoflavonifractor | 0.09±0.22 | 0.04±0.1 | 0.17±0.34 | 0.07±0.12 |
| RGIG7389 | 0.08±0.15 | 0.04±0.1 | 0.1±0.18 | 0.12±0.16 |
| UBA7488 | 0.08±0.28 | 0.03±0.15 | 0.13±0.42 | 0.11±0.21 |
| UBA3961 | 0.08±0.37 | 0.18±0.55 | 0±0 | 0±0 |
| RPPU01 | 0.08±0.75 | 0±0 | 0±0 | 0.31±1.5 |
| RGIG5057 | 0.07±0.36 | 0±0 | 0.17±0.59 | 0.09±0.25 |
| UMGS1202 | 0.07±0.14 | 0.04±0.08 | 0.1±0.16 | 0.11±0.18 |
| CAIQQL01 | 0.07±0.65 | 0.17±0.99 | 0±0 | 0±0 |
| Methanothrix | 0.07±0.68 | 0±0 | 0±0 | 0.29±1.35 |
| Egerieousia | 0.07±0.19 | 0.03±0.11 | 0.08±0.23 | 0.13±0.24 |
| UBA11358 | 0.07±0.35 | 0.16±0.52 | 0±0 | 0±0 |
| IGN3 | 0.07±0.58 | 0.16±0.88 | 0±0 | 0±0 |
| 14-2 | 0.07±0.32 | 0.02±0.08 | 0.06±0.27 | 0.15±0.56 |
| SKHV01 | 0.07±0.63 | 0±0 | 0±0 | 0.26±1.26 |
| Butyribacter | 0.06±0.61 | 0.15±0.93 | 0±0 | 0±0 |
| CAIRTM01 | 0.06±0.39 | 0.15±0.59 | 0±0 | 0±0 |
| OLB5 | 0.06±0.35 | 0.14±0.52 | 0±0 | 0±0 |
| Methylocystis | 0.06±0.28 | 0.14±0.42 | 0±0 | 0±0 |
| Robinsoniella | 0.06±0.21 | 0.02±0.08 | 0.13±0.31 | 0.05±0.19 |
| UBA2475 | 0.06±0.39 | 0.14±0.58 | 0±0 | 0±0 |
| JABFSR01 | 0.06±0.31 | 0.13±0.46 | 0±0 | 0±0 |
| Paludibacter | 0.06±0.54 | 0±0 | 0±0 | 0.23±1.07 |
| Ruthenibacterium | 0.06±0.2 | 0.12±0.29 | 0.01±0.04 | 0±0.01 |
| UBA12294 | 0.06±0.31 | 0.07±0.25 | 0.09±0.48 | 0±0 |
| Edwardsiella | 0.05±0.17 | 0.1±0.24 | 0±0 | 0.04±0.12 |
| CAJAUT01 | 0.05±0.43 | 0.12±0.65 | 0±0 | 0±0 |
| JAKAJH01 | 0.05±0.39 | 0.12±0.59 | 0±0 | 0±0 |
| CAIPTY01 | 0.05±0.28 | 0.12±0.43 | 0±0 | 0±0 |
| Romboutsia_A | 0.05±0.26 | 0.02±0.08 | 0.12±0.44 | 0.01±0.04 |
| Bacteroides_G | 0.05±0.25 | 0.12±0.37 | 0±0 | 0±0 |
| Novimethylophilus | 0.05±0.29 | 0.11±0.43 | 0±0 | 0±0 |
| Vitreimonas | 0.05±0.31 | 0.11±0.47 | 0±0 | 0±0 |
| Shewanella | 0.05±0.22 | 0.03±0.2 | 0.09±0.3 | 0.02±0.07 |
| JAERTD01 | 0.05±0.37 | 0.11±0.57 | 0±0 | 0±0 |
| JAGPHI01 | 0.05±0.25 | 0.11±0.38 | 0±0 | 0±0 |
| Aliarcobacter | 0.05±0.28 | 0.1±0.43 | 0.01±0.03 | 0±0.01 |
| CAJLXD01 | 0.05±0.19 | 0.07±0.27 | 0.03±0.08 | 0.02±0.05 |
| Methyloglobulus | 0.05±0.22 | 0.1±0.32 | 0±0 | 0±0 |
| JAHHUI01 | 0.04±0.26 | 0.01±0.04 | 0±0 | 0.17±0.51 |
| Methanocorpusculum | 0.04±0.16 | 0.06±0.2 | 0.04±0.18 | 0.03±0.06 |
| Terracidiphilus | 0.04±0.41 | 0±0 | 0±0 | 0.17±0.82 |
| Methanobacterium_A | 0.04±0.28 | 0.09±0.42 | 0±0 | 0.01±0.05 |
| DYRC01 | 0.04±0.39 | 0±0 | 0±0 | 0.16±0.79 |
| JAHHTP01 | 0.04±0.14 | 0.04±0.16 | 0.03±0.14 | 0.05±0.12 |
| RGIG5270 | 0.04±0.22 | 0±0 | 0±0 | 0.16±0.42 |
| Hylemonella | 0.04±0.38 | 0±0 | 0±0 | 0.16±0.76 |
| CALXSC01 | 0.04±0.22 | 0±0.03 | 0.01±0.02 | 0.14±0.42 |
| Eubacterium_R | 0.04±0.38 | 0.09±0.57 | 0±0 | 0±0 |
| Scatenecus | 0.04±0.15 | 0.04±0.18 | 0.02±0.09 | 0.06±0.16 |
| Copranaerobaculum | 0.04±0.16 | 0.04±0.2 | 0.04±0.11 | 0.04±0.13 |
| RFTN01 | 0.04±0.22 | 0.09±0.33 | 0±0 | 0±0 |
| JAEUNJ01 | 0.04±0.15 | 0.09±0.23 | 0±0 | 0±0 |
| OLB17 | 0.04±0.24 | 0.09±0.37 | 0±0 | 0±0 |
| Aureliella | 0.04±0.29 | 0.08±0.44 | 0±0 | 0±0 |
| FEN-979 | 0.04±0.21 | 0.08±0.31 | 0±0 | 0±0 |
| Draconibacterium | 0.04±0.16 | 0.08±0.23 | 0±0 | 0±0 |
| UBA6024 | 0.03±0.21 | 0.08±0.31 | 0±0 | 0±0 |
| Hespellia | 0.03±0.19 | 0.05±0.28 | 0.01±0.05 | 0.03±0.06 |
| Evtepia | 0.03±0.06 | 0.03±0.06 | 0.05±0.07 | 0.02±0.04 |
| Ferruginibacter | 0.03±0.15 | 0.07±0.22 | 0±0 | 0.01±0.03 |
| JAJBUQ01 | 0.03±0.06 | 0.02±0.05 | 0.02±0.06 | 0.07±0.09 |
| Anaerobium | 0.03±0.1 | 0.01±0.04 | 0.08±0.16 | 0±0 |
| SHXO01 | 0.03±0.14 | 0.07±0.21 | 0±0 | 0±0 |
| Bacilliculturomica | 0.03±0.06 | 0.02±0.06 | 0.03±0.06 | 0.04±0.08 |
| PALSA-1444 | 0.03±0.14 | 0.06±0.21 | 0±0 | 0±0 |
| MGBC133411 | 0.03±0.16 | 0±0.01 | 0.06±0.28 | 0.02±0.06 |
| 2-12-FULL-35-15 | 0.03±0.22 | 0.06±0.33 | 0±0 | 0±0 |
| Aestuariivirga | 0.03±0.11 | 0.06±0.17 | 0±0 | 0±0 |
| Syntrophorhabdus | 0.03±0.2 | 0.01±0.08 | 0±0 | 0.08±0.39 |
| Limnohabitans | 0.03±0.16 | 0.04±0.23 | 0±0 | 0.03±0.09 |
| JAAYQI01 | 0.03±0.1 | 0±0 | 0.07±0.16 | 0.02±0.06 |
| IOR16 | 0.03±0.05 | 0.02±0.06 | 0.03±0.05 | 0.03±0.05 |
| Coprobacillus | 0.02±0.07 | 0.03±0.06 | 0.03±0.1 | 0±0.01 |
| UBA5026 | 0.02±0.16 | 0±0 | 0.07±0.29 | 0±0.02 |
| Massilioclostridium | 0.02±0.08 | 0.05±0.11 | 0±0 | 0±0.02 |
| JAFGIC01 | 0.02±0.23 | 0±0 | 0±0 | 0.1±0.46 |
| CALURL01 | 0.02±0.1 | 0.02±0.09 | 0.04±0.13 | 0.01±0.03 |
| AM-1111 | 0.02±0.16 | 0.05±0.23 | 0±0 | 0±0 |
| Leadbetterella | 0.02±0.12 | 0.03±0.15 | 0.03±0.11 | 0±0 |
| Sulfuritalea | 0.02±0.13 | 0.05±0.19 | 0±0 | 0±0 |
| Aquisediminimonas | 0.02±0.11 | 0.05±0.16 | 0±0 | 0±0 |
| JAGOBP01 | 0.02±0.2 | 0±0 | 0±0 | 0.09±0.39 |
| UBA8515 | 0.02±0.12 | 0.05±0.18 | 0±0 | 0±0 |
| CHH4-2 | 0.02±0.06 | 0.01±0.05 | 0.04±0.07 | 0.02±0.05 |
| GWF2-50-10 | 0.02±0.13 | 0.05±0.2 | 0±0 | 0±0 |
| JAGOMW01 | 0.02±0.18 | 0.05±0.28 | 0±0 | 0±0 |
| Merdenecus | 0.02±0.08 | 0±0.02 | 0.06±0.14 | 0.01±0.03 |
| UBA5195 | 0.02±0.12 | 0.05±0.18 | 0±0 | 0±0 |
| Avimicrobium | 0.02±0.04 | 0.01±0.02 | 0.02±0.03 | 0.05±0.05 |
| UBA4417 | 0.02±0.19 | 0.05±0.29 | 0±0 | 0±0 |
| JACRFF01 | 0.02±0.1 | 0.05±0.15 | 0±0 | 0±0 |
| UBA3254 | 0.02±0.13 | 0.04±0.2 | 0±0 | 0±0 |
| Plesiomonas | 0.02±0.19 | 0.04±0.28 | 0±0 | 0±0 |
| GWA2-36-10 | 0.02±0.15 | 0.04±0.22 | 0±0 | 0±0 |
| Serratia_A | 0.02±0.11 | 0.02±0.06 | 0.04±0.19 | 0±0 |
| JAAYKM01 | 0.02±0.18 | 0±0 | 0±0 | 0.08±0.36 |
| RGIG4140 | 0.02±0.12 | 0±0 | 0.03±0.16 | 0.04±0.18 |
| UBA1794 | 0.02±0.08 | 0.01±0.03 | 0±0 | 0.07±0.15 |
| PALSA-1004 | 0.02±0.15 | 0.04±0.22 | 0±0 | 0±0 |
| WRDF01 | 0.02±0.05 | 0.01±0.04 | 0±0.01 | 0.06±0.09 |
| M0103 | 0.02±0.12 | 0±0 | 0±0 | 0.07±0.24 |
| Holophaga | 0.02±0.18 | 0±0 | 0±0 | 0.07±0.35 |
| MGBC102946 | 0.02±0.17 | 0.04±0.26 | 0±0 | 0±0 |
| Hepatoplasma | 0.02±0.17 | 0.04±0.26 | 0±0 | 0±0 |
| UBA1306 | 0.02±0.17 | 0±0 | 0±0 | 0.07±0.34 |
| UBA668 | 0.02±0.12 | 0.04±0.18 | 0±0 | 0±0 |
| JAFGVL01 | 0.02±0.16 | 0.04±0.25 | 0±0 | 0±0 |
| CAJATL01 | 0.02±0.1 | 0.04±0.16 | 0±0 | 0±0 |
| Fluviibacter | 0.02±0.05 | 0.03±0.07 | 0±0 | 0.02±0.05 |
| CAJBLF01 | 0.02±0.15 | 0.04±0.23 | 0±0 | 0±0 |
| UBA2192 | 0.02±0.09 | 0.02±0.08 | 0±0 | 0.03±0.14 |
| Lacibacter | 0.01±0.13 | 0.03±0.2 | 0±0 | 0±0 |
| Massiliimalia | 0.01±0.06 | 0.03±0.09 | 0±0 | 0±0 |
| CAZU01 | 0.01±0.07 | 0±0 | 0.02±0.09 | 0.03±0.09 |
| RGDT01 | 0.01±0.14 | 0.03±0.21 | 0±0 | 0±0 |
| SSEF01 | 0.01±0.1 | 0.03±0.16 | 0±0 | 0±0 |
| JAKJEI01 | 0.01±0.11 | 0.03±0.16 | 0±0 | 0±0 |
| Intestinibacillus | 0.01±0.05 | 0.02±0.05 | 0.01±0.02 | 0.02±0.06 |
| RGIG8482 | 0.01±0.08 | 0.02±0.12 | 0±0.02 | 0.01±0.03 |
| CADEED01 | 0.01±0.08 | 0.03±0.11 | 0±0 | 0±0 |
| JAAZKV01 | 0.01±0.1 | 0.03±0.15 | 0±0 | 0±0 |
| Morganella | 0.01±0.09 | 0.02±0.13 | 0.01±0.05 | 0±0 |
| JAEZVV01 | 0.01±0.09 | 0.03±0.14 | 0±0 | 0±0 |
| HGM16780 | 0.01±0.05 | 0.01±0.03 | 0.02±0.07 | 0.01±0.03 |
| JAJQEJ01 | 0.01±0.04 | 0±0.01 | 0.01±0.03 | 0.02±0.06 |
| JAAYCI01 | 0.01±0.04 | 0.02±0.06 | 0±0 | 0±0.01 |
| UBA9973 | 0.01±0.09 | 0±0 | 0±0 | 0.04±0.18 |
| Cardinium | 0.01±0.05 | 0.02±0.07 | 0±0 | 0±0 |
| Rahnella | 0.01±0.06 | 0±0 | 0±0 | 0.03±0.12 |
| Brevinema | 0.01±0.06 | 0.01±0.04 | 0.02±0.09 | 0±0 |
| Polynucleobacter | 0.01±0.03 | 0.01±0.04 | 0±0 | 0±0.01 |
| JAGQMS01 | 0.01±0.03 | 0.02±0.05 | 0±0 | 0±0 |
| Methylopumilus_A | 0.01±0.04 | 0±0 | 0±0 | 0.03±0.08 |
| UBA8529 | 0.01±0.05 | 0.01±0.07 | 0±0 | 0±0 |
| UBA11704 | 0.01±0.05 | 0.01±0.07 | 0±0 | 0±0 |
| Lumbricidophila | 0.01±0.05 | 0.01±0.08 | 0±0 | 0±0 |
| Flavobacterium | 0.01±0.05 | 0.01±0.07 | 0±0 | 0±0 |
| UBA10108 | 0.01±0.05 | 0±0 | 0±0 | 0.02±0.1 |
| Rhodoferax | 0±0.03 | 0±0 | 0±0 | 0.02±0.07 |
| Acinetobacter | 0±0.04 | 0±0 | 0.02±0.06 | 0±0 |
| C7867-006 | 0±0.04 | 0.01±0.06 | 0±0 | 0±0 |
| MWCR01 | 0±0.02 | 0.01±0.04 | 0±0 | 0±0 |
| 2-01-FULL-39-10-A | 0±0.03 | 0.01±0.04 | 0±0 | 0±0 |
| Aurantimicrobium | 0±0.01 | 0.01±0.02 | 0±0 | 0±0.01 |
| Cetobacterium_A | 0±0.02 | 0±0 | 0.01±0.03 | 0±0 |
| JACRJP01 | 0±0.02 | 0.01±0.03 | 0±0 | 0±0 |
| Vogesella | 0±0.01 | 0±0.02 | 0±0 | 0±0 |
genus_summary %>%
# left_join(sample_metadata,by=join_by(sample==sample)) %>%
mutate(genus=factor(genus, levels=rev(genus_summary_sort %>% pull(genus)))) %>%
filter(relabun > 0) %>%
ggplot(aes(x=relabun, y=genus, group=genus, color=phylum)) +
scale_color_manual(values=phylum_colors) +
geom_jitter(alpha=0.5) +
facet_grid(.~type)+
theme_minimal() +
theme(
axis.text = element_text(size=6),
)+
labs(y="Genus", x="Relative abundance", color="Phylum")
5.4.2 Per season
genus_summary %>%
group_by(genus) %>%
summarise(total_mean=mean(relabun*100, na.rm=T),
total_sd=sd(relabun*100, na.rm=T),
spring_mean=mean(relabun[season=="spring"]*100, na.rm=T),
spring_sd=sd(relabun[season=="spring"]*100, na.rm=T),
autumn_mean=mean(relabun[season=="autumn"]*100, na.rm=T),
autumn_sd=sd(relabun[season=="autumn"]*100, na.rm=T)) %>%
mutate(total=str_c(round(total_mean,2),"±",round(total_sd,2)),
spring=str_c(round(spring_mean,2),"±",round(spring_sd,2)),
autumn=str_c(round(autumn_mean,2),"±",round(autumn_sd,2))) %>%
arrange(-total_mean) %>%
dplyr::select(genus,total,spring,autumn) %>%
tt()| genus | total | spring | autumn |
|---|---|---|---|
| Bacteroides | 17.27±15.59 | 11.72±8.32 | 20.24±17.69 |
| Mucinivorans | 10.39±12.9 | 9.74±6.68 | 10.74±15.26 |
| Parabacteroides | 7.07±6.44 | 6.62±4.73 | 7.31±7.22 |
| Aeromonas | 4.15±10.69 | 4.36±9.73 | 4.04±11.25 |
| Mycoplasma_L | 3.78±6.81 | 4.07±4.75 | 3.63±7.72 |
| Rikenella | 2.79±5.08 | 4.08±5.83 | 2.11±4.53 |
| JADFUS01 | 2.22±2.02 | 2.31±1.62 | 2.18±2.22 |
| Odoribacter | 1.87±2.46 | 3±2.79 | 1.27±2.05 |
| Akkermansia | 1.63±3.1 | 3.23±4.43 | 0.77±1.54 |
| Clostridium | 1.41±1.84 | 1.64±1.83 | 1.28±1.85 |
| Chlorobaculum | 1.26±7.85 | 0±0 | 1.93±9.68 |
| UBA866 | 1.2±2.17 | 2.2±3.23 | 0.66±0.96 |
| Parabacteroides_B | 1.13±1.58 | 1.06±1.18 | 1.16±1.77 |
| Aquirickettsiella | 0.99±8.81 | 0±0 | 1.52±10.91 |
| Hafnia | 0.97±3.83 | 2.28±5.92 | 0.27±1.67 |
| Buttiauxella | 0.94±4.16 | 0.09±0.43 | 1.4±5.1 |
| Mobilisporobacter | 0.84±2.27 | 0.72±1.45 | 0.9±2.61 |
| Thiodictyon | 0.81±3.44 | 1.64±5.45 | 0.37±1.44 |
| UMGS1251 | 0.77±1.13 | 0.66±0.83 | 0.82±1.27 |
| Sarcina | 0.73±1.94 | 0.57±1.25 | 0.81±2.23 |
| Alistipes | 0.68±0.97 | 1.02±0.84 | 0.5±0.99 |
| FACHB-831 | 0.68±6.41 | 0±0 | 1.05±7.94 |
| Hydrogenoanaerobacterium | 0.66±1.76 | 0.82±1.04 | 0.58±2.05 |
| Clostridium_Q | 0.66±0.78 | 0.66±0.88 | 0.65±0.73 |
| SZUA-378 | 0.57±1.52 | 1.04±2.3 | 0.31±0.76 |
| Angelakisella | 0.56±0.72 | 0.83±0.84 | 0.41±0.61 |
| LD21 | 0.55±1.87 | 0.03±0.17 | 0.83±2.27 |
| Malacoplasma | 0.44±1.76 | 0.29±0.73 | 0.52±2.12 |
| Tidjanibacter | 0.41±0.75 | 0.31±0.35 | 0.47±0.89 |
| Hungatella_A | 0.4±0.64 | 0.28±0.61 | 0.46±0.65 |
| OLB14 | 0.39±1.69 | 0±0 | 0.6±2.06 |
| Budvicia | 0.38±1.36 | 0.27±1.15 | 0.43±1.47 |
| JAGNZR01 | 0.35±0.94 | 0.17±0.38 | 0.45±1.13 |
| Anaerorhabdus | 0.35±1.17 | 0.37±0.67 | 0.34±1.37 |
| Anaerotruncus | 0.31±0.48 | 0.25±0.33 | 0.35±0.55 |
| OM05-12 | 0.3±0.5 | 0.4±0.57 | 0.25±0.45 |
| CAIVKH01 | 0.3±2.01 | 0±0 | 0.46±2.48 |
| Chlorobium | 0.26±1.63 | 0±0 | 0.4±2.01 |
| RXIV01 | 0.25±2.33 | 0.71±3.95 | 0±0 |
| Gallalistipes | 0.25±0.71 | 0.5±1.13 | 0.11±0.22 |
| CAKVBE01 | 0.25±0.69 | 0.22±0.48 | 0.26±0.79 |
| Dielma | 0.23±0.36 | 0.29±0.4 | 0.2±0.33 |
| HGM05232 | 0.22±0.37 | 0.46±0.48 | 0.1±0.21 |
| SHND01 | 0.21±1.4 | 0.48±2.27 | 0.06±0.48 |
| Avirikenella | 0.2±0.64 | 0.24±0.45 | 0.18±0.73 |
| UBA4132 | 0.2±1.49 | 0±0 | 0.31±1.84 |
| Bilophila | 0.2±0.32 | 0.27±0.36 | 0.17±0.3 |
| Craterilacuibacter | 0.2±1.39 | 0.57±2.34 | 0±0 |
| Gallibacteroides | 0.2±0.38 | 0.37±0.53 | 0.11±0.21 |
| CAJGBR01 | 0.19±0.26 | 0.28±0.22 | 0.15±0.27 |
| Chloroploca | 0.19±1.8 | 0.54±3.06 | 0±0.01 |
| Lamprocystis | 0.18±0.88 | 0.27±0.97 | 0.13±0.82 |
| FEN-1139 | 0.18±1.71 | 0±0 | 0.27±2.12 |
| RUG14305 | 0.18±0.25 | 0.23±0.29 | 0.15±0.22 |
| Alistipes_A | 0.17±0.32 | 0.25±0.46 | 0.13±0.21 |
| Smithella | 0.17±1.55 | 0±0 | 0.26±1.92 |
| UBA6186 | 0.17±1.46 | 0.46±2.47 | 0.01±0.08 |
| Anaerovorax | 0.17±0.32 | 0.19±0.31 | 0.15±0.32 |
| Phocea | 0.16±0.35 | 0.33±0.52 | 0.07±0.18 |
| M3007 | 0.16±0.89 | 0±0 | 0.25±1.09 |
| Romboutsia_D | 0.16±0.34 | 0.28±0.49 | 0.1±0.21 |
| Cetobacterium | 0.16±0.45 | 0.13±0.33 | 0.17±0.5 |
| JADLHS01 | 0.16±0.93 | 0.22±0.86 | 0.13±0.97 |
| Scandinavium | 0.15±0.85 | 0.06±0.36 | 0.19±1.02 |
| Amedibacillus | 0.15±0.43 | 0.03±0.15 | 0.2±0.51 |
| JAGAJR01 | 0.14±0.29 | 0.21±0.29 | 0.11±0.28 |
| Luteolibacter | 0.14±0.53 | 0±0 | 0.22±0.65 |
| GCA-2737665 | 0.13±0.89 | 0±0 | 0.2±1.09 |
| Aminipila | 0.13±0.18 | 0.17±0.21 | 0.11±0.16 |
| CAIQJJ01 | 0.13±1.22 | 0±0 | 0.19±1.51 |
| JADKHC01 | 0.13±1.2 | 0±0 | 0.19±1.49 |
| JJ008 | 0.12±0.69 | 0±0 | 0.19±0.85 |
| Intestinimonas | 0.12±0.2 | 0.11±0.19 | 0.13±0.2 |
| Citrobacter | 0.12±1.12 | 0.33±1.89 | 0.01±0.07 |
| Planktothrix | 0.12±0.81 | 0.35±1.35 | 0±0.01 |
| FEN-1279 | 0.12±0.81 | 0±0 | 0.18±0.99 |
| Harryflintia | 0.12±0.32 | 0.08±0.15 | 0.13±0.38 |
| UBA5066 | 0.11±0.78 | 0.3±1.3 | 0.02±0.13 |
| JACRCG01 | 0.11±0.7 | 0±0 | 0.18±0.86 |
| Negativibacillus | 0.11±0.35 | 0.16±0.39 | 0.09±0.33 |
| Rhodoferax_C | 0.11±0.86 | 0.01±0.05 | 0.16±1.06 |
| CAIPUE01 | 0.11±0.28 | 0.15±0.26 | 0.09±0.29 |
| WRKB01 | 0.11±0.21 | 0.15±0.24 | 0.09±0.2 |
| Anaerotignum | 0.1±0.23 | 0.09±0.21 | 0.11±0.24 |
| Spyradomonas | 0.1±0.3 | 0.14±0.29 | 0.08±0.3 |
| TH-plancto1 | 0.1±0.94 | 0±0 | 0.15±1.17 |
| Azonexus | 0.09±0.43 | 0.15±0.63 | 0.06±0.28 |
| Methanoregula | 0.09±0.74 | 0±0 | 0.14±0.91 |
| Pseudoflavonifractor | 0.09±0.22 | 0.09±0.23 | 0.09±0.21 |
| RGIG7389 | 0.08±0.15 | 0.15±0.18 | 0.04±0.11 |
| UBA7488 | 0.08±0.28 | 0.21±0.43 | 0.01±0.08 |
| UBA3961 | 0.08±0.37 | 0±0 | 0.12±0.45 |
| RPPU01 | 0.08±0.75 | 0±0 | 0.12±0.93 |
| RGIG5057 | 0.07±0.36 | 0.19±0.58 | 0.01±0.07 |
| UMGS1202 | 0.07±0.14 | 0.16±0.2 | 0.03±0.06 |
| CAIQQL01 | 0.07±0.65 | 0±0 | 0.11±0.81 |
| Methanothrix | 0.07±0.68 | 0±0 | 0.11±0.84 |
| Egerieousia | 0.07±0.19 | 0.12±0.24 | 0.04±0.16 |
| UBA11358 | 0.07±0.35 | 0±0 | 0.11±0.43 |
| IGN3 | 0.07±0.58 | 0.02±0.12 | 0.09±0.72 |
| 14-2 | 0.07±0.32 | 0.15±0.53 | 0.02±0.08 |
| SKHV01 | 0.07±0.63 | 0±0 | 0.1±0.78 |
| Butyribacter | 0.06±0.61 | 0±0 | 0.1±0.76 |
| CAIRTM01 | 0.06±0.39 | 0.08±0.37 | 0.06±0.41 |
| OLB5 | 0.06±0.35 | 0±0 | 0.1±0.43 |
| Methylocystis | 0.06±0.28 | 0±0 | 0.1±0.35 |
| Robinsoniella | 0.06±0.21 | 0.02±0.07 | 0.08±0.25 |
| UBA2475 | 0.06±0.39 | 0±0 | 0.09±0.48 |
| JABFSR01 | 0.06±0.31 | 0±0 | 0.09±0.38 |
| Paludibacter | 0.06±0.54 | 0±0 | 0.09±0.67 |
| Ruthenibacterium | 0.06±0.2 | 0.06±0.23 | 0.05±0.18 |
| UBA12294 | 0.06±0.31 | 0.08±0.46 | 0.04±0.21 |
| Edwardsiella | 0.05±0.17 | 0.04±0.13 | 0.06±0.19 |
| CAJAUT01 | 0.05±0.43 | 0±0 | 0.08±0.53 |
| JAKAJH01 | 0.05±0.39 | 0±0 | 0.08±0.48 |
| CAIPTY01 | 0.05±0.28 | 0±0 | 0.08±0.35 |
| Romboutsia_A | 0.05±0.26 | 0.05±0.12 | 0.05±0.31 |
| Bacteroides_G | 0.05±0.25 | 0.1±0.4 | 0.03±0.11 |
| Novimethylophilus | 0.05±0.29 | 0±0 | 0.08±0.35 |
| Vitreimonas | 0.05±0.31 | 0±0 | 0.08±0.38 |
| Shewanella | 0.05±0.22 | 0±0 | 0.07±0.26 |
| JAERTD01 | 0.05±0.37 | 0.03±0.11 | 0.06±0.46 |
| JAGPHI01 | 0.05±0.25 | 0.01±0.03 | 0.07±0.31 |
| Aliarcobacter | 0.05±0.28 | 0.04±0.13 | 0.05±0.34 |
| CAJLXD01 | 0.05±0.19 | 0.06±0.12 | 0.04±0.22 |
| Methyloglobulus | 0.05±0.22 | 0±0 | 0.07±0.26 |
| JAHHUI01 | 0.04±0.26 | 0.12±0.43 | 0±0.03 |
| Methanocorpusculum | 0.04±0.16 | 0.02±0.05 | 0.06±0.2 |
| Terracidiphilus | 0.04±0.41 | 0±0 | 0.07±0.51 |
| Methanobacterium_A | 0.04±0.28 | 0.03±0.11 | 0.05±0.34 |
| DYRC01 | 0.04±0.39 | 0±0 | 0.06±0.49 |
| JAHHTP01 | 0.04±0.14 | 0.08±0.19 | 0.02±0.1 |
| RGIG5270 | 0.04±0.22 | 0±0.01 | 0.06±0.27 |
| Hylemonella | 0.04±0.38 | 0±0 | 0.06±0.47 |
| CALXSC01 | 0.04±0.22 | 0.05±0.22 | 0.04±0.21 |
| Eubacterium_R | 0.04±0.38 | 0±0 | 0.06±0.47 |
| Scatenecus | 0.04±0.15 | 0.02±0.09 | 0.05±0.18 |
| Copranaerobaculum | 0.04±0.16 | 0.01±0.04 | 0.06±0.19 |
| RFTN01 | 0.04±0.22 | 0±0 | 0.06±0.27 |
| JAEUNJ01 | 0.04±0.15 | 0±0 | 0.06±0.19 |
| OLB17 | 0.04±0.24 | 0.09±0.4 | 0.01±0.07 |
| Aureliella | 0.04±0.29 | 0±0 | 0.06±0.36 |
| FEN-979 | 0.04±0.21 | 0±0 | 0.06±0.25 |
| Draconibacterium | 0.04±0.16 | 0±0 | 0.05±0.19 |
| UBA6024 | 0.03±0.21 | 0±0 | 0.05±0.25 |
| Hespellia | 0.03±0.19 | 0.02±0.06 | 0.04±0.23 |
| Evtepia | 0.03±0.06 | 0.06±0.08 | 0.02±0.04 |
| Ferruginibacter | 0.03±0.15 | 0±0 | 0.05±0.18 |
| JAJBUQ01 | 0.03±0.06 | 0.04±0.07 | 0.02±0.06 |
| Anaerobium | 0.03±0.1 | 0.01±0.03 | 0.04±0.12 |
| SHXO01 | 0.03±0.14 | 0±0 | 0.04±0.18 |
| Bacilliculturomica | 0.03±0.06 | 0.04±0.08 | 0.02±0.05 |
| PALSA-1444 | 0.03±0.14 | 0±0 | 0.04±0.18 |
| MGBC133411 | 0.03±0.16 | 0.07±0.26 | 0±0.02 |
| 2-12-FULL-35-15 | 0.03±0.22 | 0±0 | 0.04±0.27 |
| Aestuariivirga | 0.03±0.11 | 0±0 | 0.04±0.14 |
| Syntrophorhabdus | 0.03±0.2 | 0±0 | 0.04±0.25 |
| Limnohabitans | 0.03±0.16 | 0±0 | 0.04±0.2 |
| JAAYQI01 | 0.03±0.1 | 0.05±0.14 | 0.01±0.06 |
| IOR16 | 0.03±0.05 | 0.03±0.05 | 0.02±0.06 |
| Coprobacillus | 0.02±0.07 | 0.01±0.04 | 0.03±0.08 |
| UBA5026 | 0.02±0.16 | 0.07±0.27 | 0±0.01 |
| Massilioclostridium | 0.02±0.08 | 0±0.02 | 0.03±0.09 |
| JAFGIC01 | 0.02±0.23 | 0±0 | 0.04±0.28 |
| CALURL01 | 0.02±0.1 | 0.04±0.13 | 0.01±0.07 |
| AM-1111 | 0.02±0.16 | 0±0 | 0.04±0.19 |
| Leadbetterella | 0.02±0.12 | 0.02±0.1 | 0.03±0.13 |
| Sulfuritalea | 0.02±0.13 | 0±0 | 0.04±0.16 |
| Aquisediminimonas | 0.02±0.11 | 0±0 | 0.04±0.13 |
| JAGOBP01 | 0.02±0.2 | 0±0 | 0.03±0.24 |
| UBA8515 | 0.02±0.12 | 0±0 | 0.03±0.15 |
| CHH4-2 | 0.02±0.06 | 0.02±0.04 | 0.02±0.07 |
| GWF2-50-10 | 0.02±0.13 | 0±0 | 0.03±0.16 |
| JAGOMW01 | 0.02±0.18 | 0±0 | 0.03±0.23 |
| Merdenecus | 0.02±0.08 | 0.02±0.04 | 0.02±0.1 |
| UBA5195 | 0.02±0.12 | 0±0 | 0.03±0.15 |
| Avimicrobium | 0.02±0.04 | 0.03±0.05 | 0.02±0.03 |
| UBA4417 | 0.02±0.19 | 0±0 | 0.03±0.24 |
| JACRFF01 | 0.02±0.1 | 0±0 | 0.03±0.12 |
| UBA3254 | 0.02±0.13 | 0±0 | 0.03±0.16 |
| Plesiomonas | 0.02±0.19 | 0.06±0.32 | 0±0 |
| GWA2-36-10 | 0.02±0.15 | 0±0 | 0.03±0.18 |
| Serratia_A | 0.02±0.11 | 0.06±0.19 | 0±0 |
| JAAYKM01 | 0.02±0.18 | 0±0 | 0.03±0.23 |
| RGIG4140 | 0.02±0.12 | 0.03±0.15 | 0.02±0.11 |
| UBA1794 | 0.02±0.08 | 0.04±0.13 | 0±0.02 |
| PALSA-1004 | 0.02±0.15 | 0±0 | 0.03±0.18 |
| WRDF01 | 0.02±0.05 | 0.01±0.04 | 0.02±0.06 |
| M0103 | 0.02±0.12 | 0±0 | 0.03±0.15 |
| Holophaga | 0.02±0.18 | 0±0 | 0.03±0.22 |
| MGBC102946 | 0.02±0.17 | 0.05±0.29 | 0±0 |
| Hepatoplasma | 0.02±0.17 | 0±0 | 0.03±0.21 |
| UBA1306 | 0.02±0.17 | 0±0 | 0.03±0.21 |
| UBA668 | 0.02±0.12 | 0±0 | 0.03±0.15 |
| JAFGVL01 | 0.02±0.16 | 0±0 | 0.03±0.2 |
| CAJATL01 | 0.02±0.1 | 0±0 | 0.03±0.13 |
| Fluviibacter | 0.02±0.05 | 0±0 | 0.02±0.06 |
| CAJBLF01 | 0.02±0.15 | 0±0 | 0.02±0.18 |
| UBA2192 | 0.02±0.09 | 0.01±0.03 | 0.02±0.1 |
| Lacibacter | 0.01±0.13 | 0±0 | 0.02±0.16 |
| Massiliimalia | 0.01±0.06 | 0±0.01 | 0.02±0.07 |
| CAZU01 | 0.01±0.07 | 0.02±0.09 | 0.01±0.05 |
| RGDT01 | 0.01±0.14 | 0±0 | 0.02±0.17 |
| SSEF01 | 0.01±0.1 | 0±0 | 0.02±0.13 |
| JAKJEI01 | 0.01±0.11 | 0±0 | 0.02±0.13 |
| Intestinibacillus | 0.01±0.05 | 0±0.01 | 0.02±0.06 |
| RGIG8482 | 0.01±0.08 | 0.03±0.13 | 0±0.02 |
| CADEED01 | 0.01±0.08 | 0±0 | 0.02±0.09 |
| JAAZKV01 | 0.01±0.1 | 0±0 | 0.02±0.12 |
| Morganella | 0.01±0.09 | 0±0 | 0.02±0.11 |
| JAEZVV01 | 0.01±0.09 | 0.03±0.16 | 0±0 |
| HGM16780 | 0.01±0.05 | 0.01±0.05 | 0.01±0.05 |
| JAJQEJ01 | 0.01±0.04 | 0.03±0.06 | 0±0.01 |
| JAAYCI01 | 0.01±0.04 | 0.01±0.04 | 0.01±0.04 |
| UBA9973 | 0.01±0.09 | 0±0 | 0.01±0.11 |
| Cardinium | 0.01±0.05 | 0±0 | 0.01±0.06 |
| Rahnella | 0.01±0.06 | 0±0 | 0.01±0.07 |
| Brevinema | 0.01±0.06 | 0.01±0.04 | 0.01±0.07 |
| Polynucleobacter | 0.01±0.03 | 0±0 | 0.01±0.04 |
| JAGQMS01 | 0.01±0.03 | 0±0 | 0.01±0.04 |
| Methylopumilus_A | 0.01±0.04 | 0±0 | 0.01±0.05 |
| UBA8529 | 0.01±0.05 | 0±0 | 0.01±0.06 |
| UBA11704 | 0.01±0.05 | 0±0 | 0.01±0.06 |
| Lumbricidophila | 0.01±0.05 | 0±0 | 0.01±0.07 |
| Flavobacterium | 0.01±0.05 | 0±0 | 0.01±0.06 |
| UBA10108 | 0.01±0.05 | 0±0 | 0.01±0.06 |
| Rhodoferax | 0±0.03 | 0±0 | 0.01±0.04 |
| Acinetobacter | 0±0.04 | 0±0 | 0.01±0.04 |
| C7867-006 | 0±0.04 | 0±0 | 0.01±0.05 |
| MWCR01 | 0±0.02 | 0±0 | 0.01±0.03 |
| 2-01-FULL-39-10-A | 0±0.03 | 0±0 | 0.01±0.04 |
| Aurantimicrobium | 0±0.01 | 0±0 | 0±0.02 |
| Cetobacterium_A | 0±0.02 | 0.01±0.03 | 0±0 |
| JACRJP01 | 0±0.02 | 0±0 | 0±0.02 |
| Vogesella | 0±0.01 | 0±0.02 | 0±0 |
genus_summary_sort <- genus_summary %>%
group_by(genus) %>%
summarise(mean=mean(relabun, na.rm=T),sd=sd(relabun, na.rm=T)) %>%
arrange(-mean) genus_summary %>%
# left_join(sample_metadata,by=join_by(sample==sample)) %>%
mutate(genus=factor(genus, levels=rev(genus_summary_sort %>% pull(genus)))) %>%
filter(relabun > 0) %>%
ggplot(aes(x=relabun, y=genus, group=genus, color=phylum)) +
scale_color_manual(values=phylum_colors) +
geom_jitter(alpha=0.5) +
facet_grid(.~season)+
theme_minimal() +
theme(
axis.text = element_text(size=6),
)+
labs(y="Genus", x="Relative abundance", color="Phylum")
5.5 Archaea
9
5.5.1 Diversity
sample richness neutral phylogenetic functional
1 EHI02583 2 1.996870 2.348233 1.279113
2 EHI02588 1 1.000000 1.000000 1.000000
3 EHI02643 1 1.000000 1.000000 1.000000
4 EHI02593 2 1.328193 1.409535 1.220665
5 EHI01585 1 1.000000 1.000000 1.000000
6 EHI02608 1 1.000000 1.000000 1.000000
7 EHI02611 1 1.000000 1.000000 1.000000
8 EHI02641 1 1.000000 1.000000 1.000000
9 EHI02571 2 1.139191 1.235919 1.081231
10 EHI02620 1 1.000000 1.000000 1.000000
11 EHI01449 1 1.000000 1.000000 1.000000
12 EHI02609 1 1.000000 1.000000 1.000000
13 EHI02572 3 2.112285 1.493212 1.293984
14 EHI01613 1 1.000000 1.000000 1.000000
15 EHI01618 1 1.000000 1.000000 1.000000
16 EHI01447 1 1.000000 1.000000 1.000000
17 EHI01627 1 1.000000 1.000000 1.000000
18 EHI02642 2 1.473791 1.756593 1.120537
19 EHI02646 4 2.604054 1.431005 1.596528
20 EHI02109 1 1.000000 1.000000 1.000000
21 EHI02579 1 1.000000 1.000000 1.000000
22 EHI02599 1 1.000000 1.000000 1.000000
23 EHI01628 1 1.000000 1.000000 1.000000
24 EHI01611 2 1.998461 1.563175 1.560517
25 EHI02637 1 1.000000 1.000000 1.000000
26 EHI01443 1 1.000000 1.000000 1.000000
27 EHI02638 3 1.730503 1.722158 1.387103
28 EHI02595 1 1.000000 1.000000 1.000000
29 EHI02574 1 1.000000 1.000000 1.000000
30 EHI02629 1 1.000000 1.000000 1.000000
31 EHI02631 1 1.000000 1.000000 1.000000
32 EHI02621 2 1.962914 1.943525 1.738397
33 EHI01442 2 1.989078 1.562265 1.554603
34 EHI02601 1 1.000000 1.000000 1.000000
35 EHI01438 NA NA NA 1.000000
36 EHI01612 NA NA NA 1.000000
37 EHI02095 NA NA NA 1.000000
38 EHI02596 NA NA NA 1.000000
39 EHI02635 NA NA NA 1.000000
40 EHI02104 NA NA NA 1.000000
41 EHI01631 NA NA NA 1.000000
42 EHI02597 NA NA NA 1.000000
43 EHI01450 NA NA NA 1.000000
44 EHI01610 NA NA NA 1.000000
45 EHI01436 NA NA NA 1.000000
46 EHI01437 NA NA NA 1.000000
47 EHI01440 NA NA NA 1.000000
48 EHI02586 NA NA NA 1.000000
49 EHI02628 NA NA NA 1.000000
50 EHI01451 NA NA NA 1.000000
51 EHI02591 NA NA NA 1.000000
52 EHI02581 NA NA NA 1.000000
53 EHI02115 NA NA NA 1.000000
54 EHI01619 NA NA NA 1.000000
55 EHI02610 NA NA NA 1.000000
56 EHI01439 NA NA NA 1.000000
57 EHI02128 NA NA NA 1.000000
58 EHI01617 NA NA NA 1.000000
59 EHI02626 NA NA NA 1.000000
60 EHI01620 NA NA NA 1.000000
61 EHI02606 NA NA NA 1.000000
62 EHI02604 NA NA NA 1.000000
63 EHI01444 NA NA NA 1.000000
64 EHI02085 NA NA NA 1.000000
65 EHI02616 NA NA NA 1.000000
66 EHI02594 NA NA NA 1.000000
67 EHI02613 NA NA NA 1.000000
68 EHI01625 NA NA NA 1.000000
69 EHI01448 NA NA NA 1.000000
70 EHI02589 NA NA NA 1.000000
71 EHI01623 NA NA NA 1.000000
72 EHI02634 NA NA NA 1.000000
73 EHI02640 NA NA NA 1.000000
74 EHI02636 NA NA NA 1.000000
75 EHI02578 NA NA NA 1.000000
76 EHI01616 NA NA NA 1.000000
77 EHI01584 NA NA NA 1.000000
78 EHI01445 NA NA NA 1.000000
79 EHI02622 NA NA NA 1.000000
80 EHI02614 NA NA NA 1.000000
81 EHI02580 NA NA NA 1.000000
82 EHI02627 NA NA NA 1.000000
83 EHI02618 NA NA NA 1.000000
84 EHI01441 NA NA NA 1.000000
85 EHI02605 NA NA NA 1.000000
86 EHI02573 NA NA NA 1.000000
87 EHI02577 NA NA NA 1.000000
88 EHI02576 NA NA NA 1.000000
89 EHI02623 NA NA NA 1.000000
90 EHI02600 NA NA NA 1.000000
91 EHI01621 NA NA NA 1.000000
92 EHI02575 NA NA NA 1.000000
